Hi Dave:
It does seem to be unrealistic to set repulsions merely between the virtual sites.
Thanks so much for your patience!
Gao J
> -----原始邮件-----
> 发件人: amber-request.ambermd.org
> 发送时间: 2020-06-02 03:00:01 (星期二)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: AMBER Digest, Vol 3020, Issue 1
>
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Using pytraj with jupyter notebook (Rangarajan, Amith)
> 2. Re: Using pytraj with jupyter notebook (Hai Nguyen)
> 3. Re: AMBER Digest, Vol 3019, Issue 1 (Gao J)
> 4. Re: AMBER Digest, Vol 3019, Issue 1 (David Cerutti)
> 5. Re: igb for non-aqueous solvent? (David A Case)
> 6. Re: igb for non-aqueous solvent? (Timothy Schutt)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 31 May 2020 19:44:17 +0000
> From: "Rangarajan, Amith" <Amith.Rangarajan.ucsf.edu>
> Subject: Re: [AMBER] Using pytraj with jupyter notebook
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <MWHPR05MB29116E10A2E3EC50B01DFC25F98D0.MWHPR05MB2911.namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello everyone,
>
> I am new to AMBER and i am trying to use pytraj.
>
> I am getting this error -"importError: dynamic module does not define module export function (PyInit_topology_objects)" when trying to use pytraj ( import pytraj) and wish to ask about what i should do to fix this?
>
>
> thanks,
> amith
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 31 May 2020 19:43:39 -0400
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] Using pytraj with jupyter notebook
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFNMPM-9HXYPZCAG5QWYhM8_S=Kte+_LcH5aq7rCG6PXC1e2Dg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Sun, May 31, 2020 at 3:44 PM Rangarajan, Amith <Amith.Rangarajan.ucsf.edu>
> wrote:
>
> > Hello everyone,
> >
> > I am new to AMBER and i am trying to use pytraj.
> >
> > I am getting this error -"importError: dynamic module does not define
> > module export function (PyInit_topology_objects)" when trying to use pytraj
> > ( import pytraj) and wish to ask about what i should do to fix this?
> >
> >
> >
> hi, it seems like you're using different python version for pytraj (saying
> use python 2 for pytraj that was compiled with python3).
>
> - which python version are you using?
> - In the notebook: import sys; print(sys.version_info)
>
> If the versions mismatch, make sure to launch the notebook with the same
> python version used for compiling pytraj.
>
> Please see the old thread: http://archive.ambermd.org/202004/0237.html
> Hai
>
>
> > thanks,
> > amith
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 1 Jun 2020 10:05:05 +0800 (GMT+08:00)
> From: "Gao J" <21919039.zju.edu.cn>
> Subject: Re: [AMBER] AMBER Digest, Vol 3019, Issue 1
> To: amber.ambermd.org
> Message-ID: <624f2f60.e8d77.1726da00ce5.Coremail.21919039.zju.edu.cn>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Dave:
> I am confused of some distinctions between your suggestion and Amber Manual.
> I think "But if you specify excl2, it's going to take your frame2 atom and say that the extra point is also 1:1 to that." means the virtual sites will inherit the interactions of the atom I have excluded.
> While in the Amber Manual, the explanation of excl[2,3] is that "The virtual site is definitively 1:1 bound to frame atom 1 and thereby inherits all 1:2, 1:3, and 1:4 neighbors of frame atom 1, but if ? is 2 or 3 then the virtual site will also be considered 1:1 to frame atoms 2 or 3 and inherit their bonded neighbors as well. This will not affect the 1:2, 1:3, and 1:4 neighbor lists of the frame atoms themselves." which I think the virtual sites will inherit the inherit the interactions except the atom I have excluded(is "?" the atom not in the excl list?). I don't know whether this problem comes from my improper understanding or the misinterpretation of the Manual.(T?T)
> Thank you once again!
>
> Best
> Gao J
>
> > -----????-----
> > ???: amber-request.ambermd.org
> > ????: 2020-06-01 03:00:01 (???)
> > ???: amber.ambermd.org
> > ??:
> > ??: AMBER Digest, Vol 3019, Issue 1
> >
> > Send AMBER mailing list submissions to
> > amber.ambermd.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lists.ambermd.org/mailman/listinfo/amber
> > or, via email, send a message with subject or body 'help' to
> > amber-request.ambermd.org
> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of AMBER digest..."
> >
> >
> > AMBER Mailing List Digest
> >
> > Today's Topics:
> >
> > 1. Re: AMBER Digest, Vol 3017, Issue 1 (Gao J)
> > 2. amber20 output header (Baker, Joseph)
> > 3. Re: amber20 output header (David Cerutti)
> > 4. Re: AMBER Digest, Vol 3017, Issue 1 (David Cerutti)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 31 May 2020 10:18:36 +0800 (GMT+08:00)
> > From: "Gao J" <21919039.zju.edu.cn>
> > Subject: Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
> > To: amber.ambermd.org
> > Message-ID: <1f7ca382.e1ef4.1726886121b.Coremail.21919039.zju.edu.cn>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Dave:
> > It's so kind of you to help me.
> > I modified my &rule file for a tentative short heating simulation of a minimized system, while "mdgx.MPI" neither returned any output nor exited with an error for a long time. The only message which seems nonlethal was that "Netcdf restart min3.rst does not ave velocity info, Warning:No velocities in restart, setting all to 0.0". I had set "irest=0" but no randam velocities assigned. Could you please have a check for what's going wrong?
> > As for your note about the interactions between virtual sites and real atoms, what if I exclude both frame1 and frame2 to keep the virtual sites out of any nonbonded interaction with real atoms? I am a newcomer of Amber and not sure if the combining rule would take these sites into consideration in this circumstance.
> > Thanks a lot for your gudiance!
> > Best
> > Gao J
> >
> > my input file:
> > &files
> > -p compw.prmtop
> > -c min3.rst
> > -xpt rule.in
> > -o eq1.out
> > -r eq1.rst
> > -x eq1.mdcrd
> > &end
> > &cntrl
> > imin=0, irest=0,nstlim=1000,dt=0.002,cut=8.0,ntb=1,ntpr=500,ntwx=500,ntt=3,gamma_ln=2.0,
> > tempi=0.0,temp0=300.0,ioutfm=1,
> > &end
> > my &rule file:
> > &rule
> > frame1="C1", frame2="C4", epname="VSB", style=1, excl1, v12=0.5, sig=2.1, eps=0.05, residue="UNK",
> > &end
> >
> > > -----????-----
> > > ???: amber-request.ambermd.org
> > > ????: 2020-05-30 03:00:01 (???)
> > > ???: amber.ambermd.org
> > > ??:
> > > ??: AMBER Digest, Vol 3017, Issue 1
> > >
> > > Send AMBER mailing list submissions to
> > > amber.ambermd.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > or, via email, send a message with subject or body 'help' to
> > > amber-request.ambermd.org
> > >
> > > You can reach the person managing the list at
> > > amber-owner.ambermd.org
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of AMBER digest..."
> > >
> > >
> > > AMBER Mailing List Digest
> > >
> > > Today's Topics:
> > >
> > > 1. Re: Amber20 pmemd.cuda installation and performance problems
> > > (David Cerutti)
> > > 2. Re: Simulating pyridine in water TIP3P (David A Case)
> > > 3. Re: Tool to calculate CSP and NOE for DNA trajectory?
> > > (Kenneth Huang)
> > > 4. Re: Small molecules paramters (Gustaf Olsson)
> > > 5. Re: adding hydrogen to pdbqt ligand files (Eduardo Mayo)
> > > 6. Amber20 Performance on RTX (Turing): known problems, with a
> > > patch forthcoming (David Cerutti)
> > > 7. questions for mdgx-virtual site (Gao J)
> > > 8. Re: questions for mdgx-virtual site (David Cerutti)
> > > 9. Re: questions for mdgx-virtual site (David Cerutti)
> > > 10. igb for non-aqueous solvent? (Timothy Schutt)
> > > 11. Re: cellulose chain (Pinky Mazumder)
> > > 12. Re: Small molecules paramters (Gustavo Seabra)
> > > 13. Re: cellulose chain (David A Case)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Thu, 28 May 2020 18:51:16 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: Re: [AMBER] Amber20 pmemd.cuda installation and performance
> > > problems
> > > To: Thomas Zeiser <thomas.zeiser.fau.de>, AMBER Mailing List
> > > <amber.ambermd.org>
> > > Message-ID:
> > > <CAEmzWj108UxHJDdvTjuGJRyr=Tj7MOjSFL3a5F+GzJVRZ75ocQ.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > I have access to a machine in Darrin York's group that has a properly
> > > situated RTX-2080Ti, and I have been able to benchmark the code and see the
> > > performance hit (also, contrary to what I reported on another thread about
> > > this, the Pascal GP100 is seeing a 5% DECREASE in performance, not an
> > > increase with Amber20, so the problem is widespread). After further
> > > consultation with Scott Legrand and one of our NVIDIA technical
> > > collaborators, we have narrowed the problem to some things that are now
> > > happening in the non-bonded kernels in order to protect us against
> > > deprecations that NVIDIA plans to make in CUDA 11 and future releases.
> > >
> > > (Thomas, thank you for your efforts, but I think we have already solved the
> > > problem, at least to the extent that testing on your platforms could inform
> > > us. I may yet log in if we devise a fix and want to test it on a broad
> > > array of RTX hardware, but that is an IF.)
> > >
> > > In particular, Scott and I looked over the kernel register spills, and
> > > Amber20 is overall better in this regard than Amber18, although neither
> > > code has a performance problem in this respect. Scott has also checked in
> > > some safer, hardware-specific kernel launch bounds and these will be
> > > applied in a future patch, but what is there is not causing a performance
> > > problem nor, that we can tell, creating any other issue. Some users, and
> > > even NVIDIA technicians themselves, have brought up possible performance
> > > drag resulting from the cmake installation as opposed to the legacy build,
> > > but I compiled with the legacy build system and I still see a 15% hit on
> > > RTX-2080Ti, so any impact of cmake is marginal.
> > >
> > > In summary, we have traced the performance hit to two kernels, and
> > > unfortunately they are the most time-consuming kernels in most MD
> > > applications. While I am still trying to understand the degree that each
> > > of the necessary changes contributes to the slowdown, the changes are not
> > > things we can simply revert, and I do not know whether even a major
> > > overhaul of the non-bonded kernel could mitigate the new CUDA calls that
> > > will be required in all code going forward. Furthermore, two years ago I
> > > attempted a major rewrite of the non-bonded routine. After climbing that
> > > mountain and reaching over the last rock, I looked down to see that the
> > > code was going to become much more complex, many niche features would have
> > > been affected, and that while it might be nice for directions I would like
> > > to see MD go, the new method was not a performance win across the board.
> > >
> > > I wish I came with better news, but it appears that this slowdown in
> > > Amber20 is about where CUDA is going, not the result of any mistakes we
> > > have made. We may be able to macro-out some of the calls for compilations
> > > to recover a few percent on legacy chips like Pascal, and the Volta
> > > architecture (V100 and Titan-V) seems to be resilient in the face of the
> > > added synchronization calls. However, it looks like the Turing
> > > architecture performance is going to suffer for the foreseeable future.
> > > The hope I can offer is that the Ampere chips on the horizon appear to
> > > resume an upward trend in the compute capacity of a single card, so in time
> > > simulations will again start to get faster.
> > >
> > > Dave
> > >
> > >
> > > On Thu, May 28, 2020 at 2:26 PM Thomas Zeiser <thomas.zeiser.fau.de> wrote:
> > >
> > > > On Wed, May 27, 2020 at 08:35:38PM +0200, Thomas Zeiser wrote:
> > > > > Hi Dave,
> > > > >
> > > > > please send me your SSH public key. I'll come back tomorrow with
> > > > > further instructions.
> > > >
> > > > you have to connect with SSH as w17p0001 to port 22622 of
> > > > grid.rrze.uni-erlangen.de
> > > > e.g. ssh -4 -p 22622 w17p0001.grid.rrze.uni-erlangen.de
> > > >
> > > > That should give you a shell on "testfront1". There, you can use e.g.
> > > > srun -w medusa --time=10:0:0 --pty /bin/bash
> > > > to get an interactive job on the node "medusa" which hosts the GPUs.
> > > >
> > > > CUDA, etc. are only installed on "medusa". Both testfront1 and
> > > > medusa can directly access data from the internet (through NAT).
> > > >
> > > > While you have a job running on medua, you can also SSH to medusa.
> > > > Once the job ends, all procces are kill. Thus, if you want to use
> > > > "screen", run it on testfront1.
> > > >
> > > > $HOME has a quota of 10 GB; $WORK of 333 GB.
> > > >
> > > >
> > > > Best
> > > >
> > > > thomas
> > > >
> > > > > Best
> > > > >
> > > > > thomas
> > > > >
> > > > > On Wed, May 27, 2020 at 02:29:58PM -0400, David Cerutti wrote:
> > > > > > This sounds like a great plan. I am about to test amber18 and amber20
> > > > on a
> > > > > > local machine in another lab. If I can get access to the server with a
> > > > > > range of different Turing GPUs I can start to look at how your problem
> > > > > > takes place.
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Dave
> > > > > >
> > > > > >
> > > > > > On Wed, May 27, 2020 at 9:08 AM Thomas Zeiser <thomas.zeiser.fau.de>
> > > > wrote:
> > > > > >
> > > > > > > Hi Dave,
> > > > > > >
> > > > > > > On Wed, May 27, 2020 at 07:54:32AM -0400, David Cerutti wrote:
> > > > > > > > I cannot make a meaningful test on an RTX-2080Ti because the card
> > > > I have
> > > > > > > > access to are not sufficiently powered to give the right numbers.
> > > > I see
> > > > > > > > about a 20% degradation relative to what Ross was able to get.
> > > > Ditto for
> > > > > > > > an RTX-6000, which is nearly as fast as a V100 despite having 20%
> > > > too
> > > > > > > > little power feeding it.
> > > > > > >
> > > > > > > we could provide you temporary access to our HPC systems to support
> > > > > > > you in investigating the prossible performance degradation.
> > > > > > >
> > > > > > > I'd could either offer one host with four different Turing-based
> > > > > > > GPUs (Geforce 2070 Super, 2080 Super, Quadro RTX 5000, and 6000) or
> > > > > > > a node with 4x Geforce 2080Ti.
> > > > > > >
> > > > > > > Both systems are running Ubuntu 18.04. Cuda toolkits 9.0 up to 10.2
> > > > > > > are installedi together with driver 440.64.00. Persistence-Mode is
> > > > > > > enabled on all GPUs. cmake/3.11.1 would also be available as
> > > > > > > module.
> > > > > > >
> > > > > > >
> > > > > > > Best
> > > > > > >
> > > > > > > thomas
> > > > > > >
> > > > > > > > Dave
> > > > > > > --
> > > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > > thomas.zeiser.fau.de
> > > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > > >
> > > > >
> > > > > --
> > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > thomas.zeiser.fau.de
> > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > >
> > > > --
> > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > thomas.zeiser.fau.de
> > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Thu, 28 May 2020 21:33:01 -0400
> > > From: David A Case <david.case.rutgers.edu>
> > > Subject: Re: [AMBER] Simulating pyridine in water TIP3P
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <20200529013301.ljprvlrh2piy3nob.vpn-client-172-16-9-226.rutgers.edu>
> > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > >
> > > On Thu, May 28, 2020, Debarati DasGupta wrote:
> > >
> > > >I faced this error in equilibration step. Should I have a smaller cut value?
> > > >Cutoff list exceeds largest sphere in unit cell!!
> > >
> > > No: you need to have a bigger system. When a side of the periodic box
> > > gets to be less than about 20 Ang., it gets to be too small for Amber to
> > > handle, since Amber was designed and optimized for larger periodic
> > > cells.
> > >
> > > You may be able to get away with setting skinnb to 1 (instead of its
> > > default value of 2). That will allow you to go to slightly smaller
> > > boxes. But it would be rather dangerous to reduce the cutoff value to
> > > anything below 8 Ang: we cut off Lennard-Jones interactions at "cut",
> > > and 8 Ang. is already on the edge of being to small.
> > >
> > > By far the simplest fix is to just use more water molecules in your
> > > original setup.
> > >
> > > ....dac
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Thu, 28 May 2020 23:57:59 -0400
> > > From: Kenneth Huang <kennethneltharion.gmail.com>
> > > Subject: Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory?
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CALeh7kALqvra6YccT-Sp4J7sMPJA37ArLhizviAkuUHjsEdrxw.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Hi Christina,
> > >
> > > Thanks a lot for the insight and script! That more or less covers for what
> > > I wanted to do NOE and CSP wise, and LAMORD should more or less fill in the
> > > gap that the protein CSP softwares I found weren't able to do.
> > >
> > > Best,
> > >
> > > Kenneth
> > >
> > > On Thu, May 28, 2020 at 8:42 AM Christina Bergonzo <cbergonzo.gmail.com>
> > > wrote:
> > >
> > > > Hi Kenneth,
> > > >
> > > > I do not know of any stand alone tools that will calculate NMR observables
> > > > from a trajectory.
> > > > I regularly do this without too much hassle using a combination of bash/awk
> > > > scripting and Cpptraj/shifts.
> > > > I also back out NOE distances from distance restraints - if you want to
> > > > predict NOEs using a trajectory, that's a different question (see Henriksen
> > > > et al. JPCB, dx.doi.org/10.1021/jp400530e), but also distance based.
> > > >
> > > > If you look at the Cpptraj distance command, there is an option for
> > > > evaluating a distance as an NOE.
> > > > I write a script that takes my atoms of interest from whatever experimental
> > > > file format I have, and formats them into the distance command:
> > > >
> > > > distance d0 :1.H1' :1.H4' type noe bound 0.0 bound 7.0 out
> > > > dist/noe.val.0.dat
> > > > ....
> > > > distance d50 :6.H5'' :6.H6 type noe bound 0.0 bound 7.0 out
> > > > dist/noe.val.50.dat
> > > > analyze statistics all out noe.dat
> > > >
> > > > The last part dumps analysis of each distance into a file (noe.dat)
> > > > containing initial and final values, avg and standard deviation, 1/r^6
> > > > averages, # of violations, etc.
> > > > Example output:
> > > >
> > > > STATISTICS :1.H1' and :1.H4'
> > > > AVERAGE: 3.0492 (0.2559 stddev)
> > > > INITIAL: 3.0944
> > > > FINAL: 3.2662
> > > > NOE SERIES: S < 2.9, M < 3.5, W < 5.0, blank otherwise.
> > > > |SMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM|
> > > > NOE < 7.00 for 100.00% of the time
> > > > NOE <r^-6>^(-1/6)= 2.9650
> > > > #Violations: Low= 0 High= 0 Total= 0
> > > > Rexp= 7.0000 <Violation>= -4.0350
> > > >
> > > > < 2.5 2.5-3.5 3.5-4.5 4.5-5.5 5.5-6.5 > 6.5
> > > > -------------------------------------------------------
> > > > %occupied | 2.4 | 95.1 | 2.5 | | | |
> > > > average | 2.402 | 3.051 | 3.611 | | | |
> > > > stddev | 0.084 | 0.223 | 0.103 | | | |
> > > > -------------------------------------------------------
> > > > __________________________________________________________________
> > > >
> > > > For chemical shifts for nucleic acids, I use shifts for protons, and
> > > > there's larmor-D for proton and carbon shifts.
> > > > And, I go through a similar procedure, where I look at the experiment to
> > > > see what's be deposited, use shifts to calculate those values from PDBs (I
> > > > have found you'll need to rename 5' and 3' ends to their non-terminal
> > > > counterparts i.e., C3 to C), and then calculate for each frame and average.
> > > >
> > > > Good luck!
> > > > -Christina
> > > >
> > > > On Wed, May 27, 2020 at 7:48 PM Kenneth Huang <kennethneltharion.gmail.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > A general question- does anyone know of tools (assuming there isn't a
> > > > > combined suite) for calculating CSP or NOEs from a trajectory? I know
> > > > > there's SPARTA+ and shiftX2 for protein CSPs for proteins, but with DNA
> > > > all
> > > > > I've seen is the NMR option in Gaussian, which seems prohibitively
> > > > > expensive.
> > > > >
> > > > > Likewise for NOEs I know of MD2NOE but haven't ever used it in context of
> > > > > DNA, and other than back-calculating from the distance restraints, I was
> > > > > just wondering if there had been any other options in cpptraj?
> > > > >
> > > > > Best,
> > > > >
> > > > > Kenneth
> > > > > --
> > > > > Ask yourselves, all of you, what power would hell have if those
> > > > imprisoned
> > > > > here could not dream of heaven?
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > -----------------------------------------------------------------
> > > > Christina Bergonzo
> > > > Research Chemist
> > > > Biomolecular Measurement Division, MML, NIST
> > > > -----------------------------------------------------------------
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > Ask yourselves, all of you, what power would hell have if those imprisoned
> > > here could not dream of heaven?
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Fri, 29 May 2020 05:53:03 +0000
> > > From: Gustaf Olsson <gustaf.olsson.lnu.se>
> > > Subject: Re: [AMBER] Small molecules paramters
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID: <EDDA8042-177F-409D-9875-76E4A5AA9EF2.lnu.se>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > According to the fifth information webpage
> > >
> > > ?Amber-compatible parameters can also be generated, although Amber-style force field files are not output (users can convert though with parmed)?
> > > - http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> > >
> > > It should be very possible. If it is advisable, I suspect that depends on the quality of generated parameters.
> > >
> > > Best regards
> > > // Gustaf
> > >
> > >
> > > On 28 May 2020, at 14:47, Athena N <athena.nas01.gmail.com<mailto:athena.nas01.gmail.com>> wrote:
> > >
> > > Hi all,
> > >
> > > I want to know if it advisable to use any other force fields than gaff for
> > > small molecules like some indole and pyridine systems.? If we generate some
> > > parameters using fftk (force field tool kit), could we use those and do the
> > > simulation in AMBER?
> > >
> > > Thank you all
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Fri, 29 May 2020 02:25:00 -0400
> > > From: Eduardo Mayo <eduardomayoyanes.gmail.com>
> > > Subject: Re: [AMBER] adding hydrogen to pdbqt ligand files
> > > To: amber.ambermd.org
> > > Message-ID:
> > > <CAFVrw=SeTENo9zGCZO3vHbQ=ruZGs8HFYVJNv6WYqY2yaMwxyw.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Hi!
> > > I recommend:
> > > 1 convert to .mol file using babel (with and without -h) and check if the
> > > tautomeric state is the desired.
> > > 2 if 1 didn't work then covert to smarts or smiles( so if you got a
> > > tautomeric state with local charge the smarts/smiles will have this
> > > information) . Use rdkit to covert smiles/smarts to rdkit.Mol and add then
> > > the hydrogen. Chem.Embedded the molecule so you have a 3D model. The read
> > > the mol file using Chem.MolFromMolFile. Align (you may need find the mcse)
> > > the molecule obtained from smiles to the molecule obtained from the mol
> > > file.
> > >
> > >
> > >
> > >
> > > Message: 3
> > > Date: Tue, 28 Apr 2020 21:15:36 +0000 (UTC)
> > > From: Marawan Hussien <marawanhussain.yahoo.com>
> > > Subject: [AMBER] adding hydrogen to pdbqt ligand files
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID: <1174479232.1819345.1588108536730.mail.yahoo.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Is there is a standard leap command to add hydrogen atoms to non-polar
> > > atoms (carbons) only during system building? I am preparing a
> > > protein-ligand system for MD from pdbqt protein-ligand complex and do not
> > > want to change the ligand tautomeric state.? I tried rdkit, obabel, chimera
> > > but every tool I tried will add hydrogen to the entire molecule, not carbon
> > > atoms only? Any suggestion?
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 6
> > > Date: Fri, 29 May 2020 02:30:20 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: [AMBER] Amber20 Performance on RTX (Turing): known problems,
> > > with a patch forthcoming
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAEmzWj2pfjPxJg0-O+th+VyMcBsjFhqERfM0AJDtxZAzps6v2Q.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Dear Users,
> > >
> > > As has been shared on this listserv, many users are finding that Amber20 is
> > > not as fast on Turing architectures for PME simulations as Amber18. The
> > > source of this problem has now been identified, and indeed it affects much
> > > more than just Turing, but the 15-20% slowdown seen on Turing is merely the
> > > most severe case.
> > >
> > > The slowdown itself does NOT reflect any bugs or issues that would
> > > necessitate repeating experiments. The problem, rather, is that some
> > > future-proofing that our collaborators at NVIDIA kindly performed for us
> > > has led to more GPU effort in synchronization. The benefit of this is
> > > that, come CUDA 11 and the new Ampere chipset, pmemd.cuda is already
> > > prepared to run on the cards (at a substantially greater speed than is
> > > currently possible with a V100, which in my view competes with RTX-6000 for
> > > top dog). However, legacy chipsets that do not need to perform the
> > > synchronization required for CUDA 11 to work properly will suffer in
> > > performance.
> > >
> > > Contrary to what I warned yesterday afternoon, a fix is possible and we
> > > already have it. A compiler-specific directive will create separate code
> > > paths for the various chipsets and mask out the synchronization where it is
> > > not needed, recovering the Amber18 performance while still keeping the code
> > > in a state that is ready for the next architecture.
> > >
> > > I would like to thank Scott Legrand, Peng Wang, and others at NVIDIA who
> > > contributed either to the future-proofing or the short-term recovery
> > > effort. As you sit at home preparing your new simulations, please enjoy
> > > some ice cream or other simple treat while you await the forthcoming patch
> > > that will put Amber20 back where it should be on the benchmarks.
> > >
> > > Sincerely,
> > >
> > > Dave Cerutti
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 7
> > > Date: Fri, 29 May 2020 16:29:44 +0800 (GMT+08:00)
> > > From: "Gao J" <21919039.zju.edu.cn>
> > > Subject: [AMBER] questions for mdgx-virtual site
> > > To: amber.ambermd.org
> > > Message-ID: <59110ff3.e289d.1725f8d21aa.Coremail.21919039.zju.edu.cn>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Hello
> > >
> > > I want to perform mix-solvent MD in amber and to prevent aggregation ofbenzene probes, I need to set virtual sites on the probes with L-J repulsions between themselves merely. My parameters for &rule were as follows and I got an error said "ReadEPRuleFile >> Error. Extra point name unspecified." So I wonder what the correct format of "epname" or "atom" required. What's more, I am a little confused if any parameters needed for "excl[1,2]".
> > >
> > > I really appreciate for your help!
> > >
> > > &rule
> > >
> > > frame[1,2]: C1 C4
> > >
> > > epname: VSB
> > >
> > > atom: VSB
> > >
> > > style: 1
> > >
> > > excl[1,2]
> > >
> > > v12: 0.5
> > >
> > > Sig: 21
> > >
> > > eps: 0.01
> > >
> > > residue: UNK
> > >
> > > &end
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 8
> > > Date: Fri, 29 May 2020 05:42:42 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAEmzWj1n-DX_UodrWv9srcjbPRDDb03vmabfuFwTo5Rau6SO3w.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > OK, so good evening! mdgx is not going to be FAST simulator but if you
> > > just need to get a system running a few thousand (or even million) steps of
> > > MD then it'll do fine. I am working right now to enable this virtual site
> > > functionality in pmemd and also tleap, so with luck it'll be possible to
> > > create more interesting molecular models in the standard MD engines soon.
> > >
> > > For the &rule namelist, it's... a &namelist, just like &cntrl or &ewald in
> > > the sander and pmemd programs. The parser I wrote for it is not
> > > technically the Fortran standard, but it gets things pretty well and lets
> > > you have some flexibility. I would try writing this first:
> > >
> > > &rule
> > > frame1 = "C1",
> > > frame2 = "C2",
> > > epname = "VSB",
> > > style = 1,
> > > v12 = 0.5,
> > > sig = 2.1,
> > > eps = 0.05,
> > > residue = "UNK",
> > > &end
> > >
> > > In your input, you have lots of colon punctuation (:) that mdgx won't know
> > > how to parse (nor will sander or pmemd). And I've written the above in
> > > shorthand. There are aliases for all those keywords if you find one or the
> > > other easier to remember ("sig" can also be "Sigma"), but the keywords ARE
> > > case-sensitive. The "epname" keyword actually has four aliases, "epname",
> > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard there.)
> > >
> > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > points: if they're right on the middle of a bond, or equally close to more
> > > than one real atom in general, how do we count their exclusions? (This is a
> > > reason that one of the experienced force field developers I work with
> > > demands that all of these extra points be close to their ONE parent atom
> > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > definition, an extra point is 1:1 to its parent atom, so all non-bonded
> > > exclusions of the frame1 atom will be inherited by the extra point. But if
> > > you specify excl2, it's going to take your frame2 atom and say that the
> > > extra point is also 1:1 to that. Ditto for excl3, so the extra point is
> > > accumulating more and more exclusions, atoms that it will not count
> > > interactions with.
> > >
> > > This makes me realize that I need to document this part of the code a bit
> > > better, specifically in the onboard manual. There are descriptions for all
> > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command line.
> > > But not for &rule...
> > >
> > > Happy to help more, and you are not the first to make use of mdgx to create
> > > some very unorthodox (not unusual, just not what the typical programs
> > > simulate) molecular models. It HAS been done before, and not just by me :-)
> > >
> > > Dave
> > >
> > >
> > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > >
> > > > Hello
> > > >
> > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > repulsions between themselves merely. My parameters for &rule were as
> > > > follows and I got an error said "ReadEPRuleFile >> Error. Extra point name
> > > > unspecified." So I wonder what the correct format of "epname" or "atom"
> > > > required. What's more, I am a little confused if any parameters needed for
> > > > "excl[1,2]".
> > > >
> > > > I really appreciate for your help!
> > > >
> > > > &rule
> > > >
> > > > frame[1,2]: C1 C4
> > > >
> > > > epname: VSB
> > > >
> > > > atom: VSB
> > > >
> > > > style: 1
> > > >
> > > > excl[1,2]
> > > >
> > > > v12: 0.5
> > > >
> > > > Sig: 21
> > > >
> > > > eps: 0.01
> > > >
> > > > residue: UNK
> > > >
> > > > &end
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 9
> > > Date: Fri, 29 May 2020 05:49:46 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAEmzWj3n5=jWdmadVwoi-DVsCWC90bGnhNQ7440eWsoDWEPLnQ.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Another note: if you are trying to simulate a mixture of two solvents and
> > > finding that the two molecular models do not want to stay mixed, this is a
> > > well-known problem in many models. If you want to just have virtual sites
> > > (extra points) sticking out of the benzene to push benzenes away from each
> > > other, that's one way to do it but it sounds extremely "staged" shall we
> > > say. It would be like you've contrived the model and getting any useful
> > > properties out of it would be a hard sell. I'm not actually sure you could
> > > do this--mdgx is going to see the LJ parameters you assign to the virtual
> > > sites and then try to apply the reigning LJ combining rule to determine how
> > > they interact with other atoms. So they'd interact with ALL other atoms of
> > > the simulation according to Lorentz-Berthelot combining rules, I expect,
> > > not just other virtual sites.
> > >
> > > Dave
> > >
> > >
> > > On Fri, May 29, 2020 at 5:42 AM David Cerutti <dscerutti.gmail.com> wrote:
> > >
> > > > OK, so good evening! mdgx is not going to be FAST simulator but if you
> > > > just need to get a system running a few thousand (or even million) steps of
> > > > MD then it'll do fine. I am working right now to enable this virtual site
> > > > functionality in pmemd and also tleap, so with luck it'll be possible to
> > > > create more interesting molecular models in the standard MD engines soon.
> > > >
> > > > For the &rule namelist, it's... a &namelist, just like &cntrl or &ewald in
> > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > technically the Fortran standard, but it gets things pretty well and lets
> > > > you have some flexibility. I would try writing this first:
> > > >
> > > > &rule
> > > > frame1 = "C1",
> > > > frame2 = "C2",
> > > > epname = "VSB",
> > > > style = 1,
> > > > v12 = 0.5,
> > > > sig = 2.1,
> > > > eps = 0.05,
> > > > residue = "UNK",
> > > > &end
> > > >
> > > > In your input, you have lots of colon punctuation (:) that mdgx won't know
> > > > how to parse (nor will sander or pmemd). And I've written the above in
> > > > shorthand. There are aliases for all those keywords if you find one or the
> > > > other easier to remember ("sig" can also be "Sigma"), but the keywords ARE
> > > > case-sensitive. The "epname" keyword actually has four aliases, "epname",
> > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard there.)
> > > >
> > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > points: if they're right on the middle of a bond, or equally close to more
> > > > than one real atom in general, how do we count their exclusions? (This is a
> > > > reason that one of the experienced force field developers I work with
> > > > demands that all of these extra points be close to their ONE parent atom
> > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > definition, an extra point is 1:1 to its parent atom, so all non-bonded
> > > > exclusions of the frame1 atom will be inherited by the extra point. But if
> > > > you specify excl2, it's going to take your frame2 atom and say that the
> > > > extra point is also 1:1 to that. Ditto for excl3, so the extra point is
> > > > accumulating more and more exclusions, atoms that it will not count
> > > > interactions with.
> > > >
> > > > This makes me realize that I need to document this part of the code a bit
> > > > better, specifically in the onboard manual. There are descriptions for all
> > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command line.
> > > > But not for &rule...
> > > >
> > > > Happy to help more, and you are not the first to make use of mdgx to
> > > > create some very unorthodox (not unusual, just not what the typical
> > > > programs simulate) molecular models. It HAS been done before, and not just
> > > > by me :-)
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > >
> > > >> Hello
> > > >>
> > > >> I want to perform mix-solvent MD in amber and to prevent aggregation
> > > >> ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > >> repulsions between themselves merely. My parameters for &rule were as
> > > >> follows and I got an error said "ReadEPRuleFile >> Error. Extra point name
> > > >> unspecified." So I wonder what the correct format of "epname" or "atom"
> > > >> required. What's more, I am a little confused if any parameters needed for
> > > >> "excl[1,2]".
> > > >>
> > > >> I really appreciate for your help!
> > > >>
> > > >> &rule
> > > >>
> > > >> frame[1,2]: C1 C4
> > > >>
> > > >> epname: VSB
> > > >>
> > > >> atom: VSB
> > > >>
> > > >> style: 1
> > > >>
> > > >> excl[1,2]
> > > >>
> > > >> v12: 0.5
> > > >>
> > > >> Sig: 21
> > > >>
> > > >> eps: 0.01
> > > >>
> > > >> residue: UNK
> > > >>
> > > >> &end
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 10
> > > Date: Fri, 29 May 2020 08:40:59 -0500
> > > From: Timothy Schutt <tschutt7.gmail.com>
> > > Subject: [AMBER] igb for non-aqueous solvent?
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAGGi8+gfyC=aCWfrDO+8oEpWCOzyTBnGQqUja4yv=9w1o2Bm5A.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Hi Amber Folks!
> > >
> > > Is it an okay approximation to use igb=1 and extdiel=*dielectric value* to
> > > represent a non-aqueous solvent implicitly?
> > >
> > > I would like to investigate some surface binding interactions of a
> > > non-aqueous solvent but the solvents are too viscous to get decent sampling
> > > in a reasonable time frame so my thought was to use 2D umbrella sampling
> > > across the surface sites using just one explicit solvent molecule with the
> > > rest being implicit. In each solvent system I would use the different one
> > > explicit solvent and the approrpiate external dielectric for that solvent
> > > in bulk. Would that be an accurate enough approach to provide reliable
> > > trends of mapping different solvents interactions with the surface?
> > >
> > > Any advice is greatly appreciated, Thanks!
> > >
> > > -Tim
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 11
> > > Date: Fri, 29 May 2020 09:46:58 -0500
> > > From: Pinky Mazumder <pmazumder67.gmail.com>
> > > Subject: Re: [AMBER] cellulose chain
> > > To: AMBER Mailing List <amber.ambermd.org>, Lachele Foley
> > > <lf.list.gmail.com>
> > > Message-ID:
> > > <CAFoDHbjw9EqX4ewswc+agnru_2pRMZR2kssyXzUjW0u5x7GRQw.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Thank you.
> > >
> > > I can place the chains parallel to each other. After that, I need to see
> > > the h-bond interaction between the polymers. For that I ran the simulations
> > > with energy minimization, heating and production MD.
> > >
> > > Even after, I do not see the H-Bond. To do so, what process I need to
> > > follow?
> > >
> > > Thank you.
> > >
> > > Sincerely,
> > > Pinky
> > >
> > > On Sat, May 16, 2020 at 4:33 AM Lachele Foley <lf.list.gmail.com> wrote:
> > >
> > > > When you copy the chains, they have exactly the same x,y,z
> > > > coordinates. In other words, they are right on top of each other.
> > > >
> > > > You will need to use the translate and/or transpose commands to put
> > > > them into the proper relative geometries.
> > > >
> > > > On Fri, May 15, 2020 at 11:53 PM Pinky Mazumder <pmazumder67.gmail.com>
> > > > wrote:
> > > > >
> > > > > Please discard my previous message.
> > > > >
> > > > >
> > > > > Thank you so much for your cordial response.
> > > > >
> > > > >
> > > > > I can copy the chain using this command and the numbers of atoms are
> > > > > increasing.
> > > > >
> > > > >
> > > > > However, I am not able to see the two chains together in vmd or in the
> > > > > xleap using the edit command.
> > > > >
> > > > >
> > > > > Could you please help me in this regard?
> > > > >
> > > > >
> > > > > Thank you again.
> > > > >
> > > > > Sincerely,
> > > > > Pinky
> > > > >
> > > > > On Fri, May 15, 2020 at 10:51 PM Pinky Mazumder <pmazumder67.gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Thank you so much for your cordial response.
> > > > > >
> > > > > >
> > > > > > But, I can show the two chains together using vmd. I can copying the
> > > > chain
> > > > > > because the numbers of atoms are increasing.
> > > > > >
> > > > > >
> > > > > > However, I am not able to see the two chains together.
> > > > > >
> > > > > >
> > > > > > Could you please help me in this regard?
> > > > > >
> > > > > >
> > > > > > Thank you again.
> > > > > >
> > > > > > Sincerely,
> > > > > >
> > > > > > On Fri, May 15, 2020 at 10:09 PM Lachele Foley <lf.list.gmail.com>
> > > > wrote:
> > > > > >
> > > > > >> First, you need to know the geometric relationships between the
> > > > > >> chains. The relationships will differ based on the source of the
> > > > > >> cellulose.
> > > > > >>
> > > > > >> In leap, you can use:
> > > > > >>
> > > > > >> chain2 = copy chain1
> > > > > >>
> > > > > >> to make a copy of a chain.
> > > > > >>
> > > > > >> Then, once you know the relative geometries, you can use translate
> > > > > >> and/or transform to position the chains properly with respect to each
> > > > > >> other.
> > > > > >>
> > > > > >> Alternatively, find an experimentally-determined structure, such as an
> > > > > >> X-ray or cryo-EM structure.
> > > > > >>
> > > > > >> Also consider contacting Dr. Jodi Hadden. She can probably help you,
> > > > > >> but she's pretty busy with other stuff, so you might have to be
> > > > > >> patient.
> > > > > >>
> > > > > >> On Fri, May 15, 2020 at 1:01 PM Pinky Mazumder <pmazumder67.gmail.com
> > > > >
> > > > > >> wrote:
> > > > > >> >
> > > > > >> > Hi David,
> > > > > >> >
> > > > > >> >
> > > > > >> > Thank you for your response.
> > > > > >> >
> > > > > >> >
> > > > > >> >
> > > > > >> > I have been able to make the polymer of cellulose. But I need
> > > > multiple
> > > > > >> > chains together.
> > > > > >> >
> > > > > >> >
> > > > > >> > Could you please suggest how can I replicate the same polymer chain
> > > > or
> > > > > >> can
> > > > > >> > I build the multiple number of polymer chain together?
> > > > > >> >
> > > > > >> >
> > > > > >> > Is there any specific tutorial or command that I need to follow?
> > > > > >> >
> > > > > >> >
> > > > > >> > Thank you.
> > > > > >> >
> > > > > >> >
> > > > > >> > Kind regards,
> > > > > >> >
> > > > > >> > Pinky
> > > > > >> >
> > > > > >> > On Sun, Apr 5, 2020, 12:20 PM David A Case <david.case.rutgers.edu>
> > > > > >> wrote:
> > > > > >> >
> > > > > >> > > On Thu, Apr 02, 2020, Pinky Mazumder wrote:
> > > > > >> > > >
> > > > > >> > > >I want to build a chain of cellulose. So when I am trying to do
> > > > this
> > > > > >> by
> > > > > >> > > >using foo sequence command.
> > > > > >> > > >
> > > > > >> > > > It says that '' Error : sequence : ILLEGAL UNIT named Glc''.
> > > > > >> > >
> > > > > >> > > Are you inside tleap at this point? If so, execute the "list"
> > > > > >> command,
> > > > > >> > > and see if Glc is one of the units listed. If not, you would
> > > > need to
> > > > > >> > > somehow load the units you want.
> > > > > >> > >
> > > > > >> > > Carbohydrates are discussed in Chap. 3 of the Amber Reference
> > > > Manual:
> > > > > >> > > you might see if that would help.
> > > > > >> > >
> > > > > >> > > If this is not a tleap error, then please give more details about
> > > > > >> > > exactly what you mean by "using foo sequence command".
> > > > > >> > >
> > > > > >> > > ...thx...dac
> > > > > >> > >
> > > > > >> > >
> > > > > >> > > _______________________________________________
> > > > > >> > > AMBER mailing list
> > > > > >> > > AMBER.ambermd.org
> > > > > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> > >
> > > > > >> > _______________________________________________
> > > > > >> > AMBER mailing list
> > > > > >> > AMBER.ambermd.org
> > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --
> > > > > >> :-) Lachele
> > > > > >> Lachele Foley
> > > > > >> CCRC/UGA
> > > > > >> Athens, GA USA
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> AMBER mailing list
> > > > > >> AMBER.ambermd.org
> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Pinky, Sharmi
> > > > > > AL,US
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Pinky, Sharmi
> > > > > AL,US
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > >
> > > > --
> > > > :-) Lachele
> > > > Lachele Foley
> > > > CCRC/UGA
> > > > Athens, GA USA
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > Pinky, Sharmi
> > > AL,US
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 12
> > > Date: Fri, 29 May 2020 12:20:56 -0400
> > > From: Gustavo Seabra <gustavo.seabra.gmail.com>
> > > Subject: Re: [AMBER] Small molecules paramters
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAO4guEKk=2u1gnzrdBp8hSCDsV5yaN2Q52Muip+SW3_QcOW_hg.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Although it is possible to convert parameters to AMBER *format*, so they
> > > can be read by AMBER, this is not the ideal. Bear in mind that the MD force
> > > fields rely on a fine balance between charges and force constants
> > > obtained from multiple calculations, and that each force field "flavor"
> > > uses a different methodology to obtain those parameters. So, ideally, you
> > > will want to use for your small molecule the same methodology that was used
> > > to derive parameters for the rest of the system, or at least have some
> > > indication that the parameters are compatible. GAFF (ad GAFF2) have been
> > > developed with that in mind, so their parameters are, in principle,
> > > compatible with the Amber force fields. If you get the parameters from
> > > other sources, make sure you do some extra testing.
> > >
> > > All the best,
> > > --
> > > Gustavo Seabra.
> > >
> > >
> > > On Thu, May 28, 2020 at 8:47 AM Athena N <athena.nas01.gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I want to know if it advisable to use any other force fields than gaff for
> > > > small molecules like some indole and pyridine systems.? If we generate some
> > > > parameters using fftk (force field tool kit), could we use those and do the
> > > > simulation in AMBER?
> > > >
> > > > Thank you all
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 13
> > > Date: Fri, 29 May 2020 12:32:06 -0400
> > > From: David A Case <david.case.rutgers.edu>
> > > Subject: Re: [AMBER] cellulose chain
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <20200529163206.k2wr3wlvv2kcwtee.vpn-client-172-16-9-226.rutgers.edu>
> > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > >
> > > On Fri, May 29, 2020, Pinky Mazumder wrote:
> > > >
> > > >I can place the chains parallel to each other. After that, I need to see
> > > >the h-bond interaction between the polymers. For that I ran the simulations
> > > >with energy minimization, heating and production MD.
> > > >
> > > >Even after, I do not see the H-Bond. To do so, what process I need to
> > > >follow?
> > >
> > > I guessing you need a better starting structure. Do the chains move
> > > much during the simulation? If there are no inter-chain hydrogen bonds
> > > in the starting structure, it may difficult to get them to form just
> > > with MD, even if the H-bonded structure has a lower free energy.
> > >
> > > You may be able to get some good ideas, plus a feeling for how mobile
> > > your chains are, by looking at the trajectories you have. Generally, MD
> > > simluations sample configurations close to the starting point, and
> > > either long simulations or advanced sampling methods are required to
> > > find quite different structures.
> > >
> > > If you know what H-bonds you would like to form, you could add
> > > restraints (called "NMR" restraints in Amber lingo, for historical
> > > reasons) that will pull the H-bond donor and acceptor atoms to an
> > > H-bonding geometry.
> > >
> > > ....good luck...dac
> > >
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > End of AMBER Digest, Vol 3017, Issue 1
> > > **************************************
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sat, 30 May 2020 22:18:49 -0400
> > From: "Baker, Joseph" <bakerj.tcnj.edu>
> > Subject: [AMBER] amber20 output header
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAA5VDpDRkhf2OffxXdNd1dXZxA=Nu9wv580Go8+JUMuKDLEE4Q.mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi all,
> >
> > In my output log files when running pmemd.cuda in Amber20 I get the
> > following (Amber 20 PMEMD but then a comment about release 18). pmemd
> > --version says Version 20 in this case.
> >
> > ------------------------------------------------------- Amber 20 PMEMD 2020
> > -------------------------------------------------------| PMEMD
> > implementation of SANDER, Release 18
> >
> > But this made me curious, and I've noticed too that when looking at some of
> > my Amber18 output logs in the output it reports Amber 18 and Release 18,
> > but doing pmemd --version with Amber18 loaded reports Version 16.
> >
> > Are these just misprints in the output header info (for version 20) and in
> > the version info for Amber18?
> >
> > Thanks!
> > Joe
> >
> > ------
> > Joseph Baker, PhD
> > Associate Professor
> > Department of Chemistry
> > C212 Science Complex
> > The College of New Jersey
> > Ewing, NJ 08628
> > Phone: (609) 771-3173
> > Web: http://bakerj.pages.tcnj.edu/
> > Pronouns: he/him/his
> >
> > Chair (2020), Trenton Local Section of the ACS
> > Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> > Research
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Sat, 30 May 2020 23:56:46 -0400
> > From: David Cerutti <dscerutti.gmail.com>
> > Subject: Re: [AMBER] amber20 output header
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEmzWj1KSEHGjSi5_F319cTcN=_tuimWH0+7WcjK8eSHU3_VOw.mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > I'm currently without network access to the code, but this looks like a
> > misprint in both cases. Someone, like me, could do a 'grep " 18 " src/*/*'
> > command to see all instances of that 18. But please be assured, you've got
> > Amber20.
> >
> > Dave
> >
> >
> > On Sat, May 30, 2020 at 10:19 PM Baker, Joseph <bakerj.tcnj.edu> wrote:
> >
> > > Hi all,
> > >
> > > In my output log files when running pmemd.cuda in Amber20 I get the
> > > following (Amber 20 PMEMD but then a comment about release 18). pmemd
> > > --version says Version 20 in this case.
> > >
> > > ------------------------------------------------------- Amber 20 PMEMD 2020
> > > -------------------------------------------------------| PMEMD
> > > implementation of SANDER, Release 18
> > >
> > > But this made me curious, and I've noticed too that when looking at some of
> > > my Amber18 output logs in the output it reports Amber 18 and Release 18,
> > > but doing pmemd --version with Amber18 loaded reports Version 16.
> > >
> > > Are these just misprints in the output header info (for version 20) and in
> > > the version info for Amber18?
> > >
> > > Thanks!
> > > Joe
> > >
> > > ------
> > > Joseph Baker, PhD
> > > Associate Professor
> > > Department of Chemistry
> > > C212 Science Complex
> > > The College of New Jersey
> > > Ewing, NJ 08628
> > > Phone: (609) 771-3173
> > > Web: http://bakerj.pages.tcnj.edu/
> > > Pronouns: he/him/his
> > >
> > > Chair (2020), Trenton Local Section of the ACS
> > > Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> > > Research
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Sat, 30 May 2020 23:59:36 -0400
> > From: David Cerutti <dscerutti.gmail.com>
> > Subject: Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEmzWj3WAjLMW5FpPvdAxHu8wPHSZoTWOhs6k2wbuXja-1xsqQ.mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Please just understand that you're using a pretty old feature here: mdgx,
> > despite the name, is a force field oriented program. The MD capability is
> > merely subservient to model building and parameter fitting. I would try to
> > run with serial (uniprocessor) mdgx until you know that everything works.
> > If you call excl1 and excl2, the virtual sites (also known as extra points)
> > will inherit all of the bonded exclusions of those frame atoms. But they
> > will make non-bonded interactions will all OTHER atoms in the system,
> > including other virtual sites and other atoms with mass, on other molecules.
> >
> > Dave
> >
> >
> > On Sat, May 30, 2020 at 10:19 PM Gao J <21919039.zju.edu.cn> wrote:
> >
> > > Hi Dave:
> > > It's so kind of you to help me.
> > > I modified my &rule file for a tentative short heating simulation of a
> > > minimized system, while "mdgx.MPI" neither returned any output nor exited
> > > with an error for a long time. The only message which seems nonlethal was
> > > that "Netcdf restart min3.rst does not ave velocity info, Warning:No
> > > velocities in restart, setting all to 0.0". I had set "irest=0" but no
> > > randam velocities assigned. Could you please have a check for what's going
> > > wrong?
> > > As for your note about the interactions between virtual sites and real
> > > atoms, what if I exclude both frame1 and frame2 to keep the virtual sites
> > > out of any nonbonded interaction with real atoms? I am a newcomer of Amber
> > > and not sure if the combining rule would take these sites into
> > > consideration in this circumstance.
> > > Thanks a lot for your gudiance!
> > > Best
> > > Gao J
> > >
> > > my input file:
> > > &files
> > > -p compw.prmtop
> > > -c min3.rst
> > > -xpt rule.in
> > > -o eq1.out
> > > -r eq1.rst
> > > -x eq1.mdcrd
> > > &end
> > > &cntrl
> > > imin=0,
> > > irest=0,nstlim=1000,dt=0.002,cut=8.0,ntb=1,ntpr=500,ntwx=500,ntt=3,gamma_ln=2.0,
> > > tempi=0.0,temp0=300.0,ioutfm=1,
> > > &end
> > > my &rule file:
> > > &rule
> > > frame1="C1", frame2="C4", epname="VSB", style=1, excl1, v12=0.5, sig=2.1,
> > > eps=0.05, residue="UNK",
> > > &end
> > >
> > > > -----????-----
> > > > ???: amber-request.ambermd.org
> > > > ????: 2020-05-30 03:00:01 (???)
> > > > ???: amber.ambermd.org
> > > > ??:
> > > > ??: AMBER Digest, Vol 3017, Issue 1
> > > >
> > > > Send AMBER mailing list submissions to
> > > > amber.ambermd.org
> > > >
> > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > or, via email, send a message with subject or body 'help' to
> > > > amber-request.ambermd.org
> > > >
> > > > You can reach the person managing the list at
> > > > amber-owner.ambermd.org
> > > >
> > > > When replying, please edit your Subject line so it is more specific
> > > > than "Re: Contents of AMBER digest..."
> > > >
> > > >
> > > > AMBER Mailing List Digest
> > > >
> > > > Today's Topics:
> > > >
> > > > 1. Re: Amber20 pmemd.cuda installation and performance problems
> > > > (David Cerutti)
> > > > 2. Re: Simulating pyridine in water TIP3P (David A Case)
> > > > 3. Re: Tool to calculate CSP and NOE for DNA trajectory?
> > > > (Kenneth Huang)
> > > > 4. Re: Small molecules paramters (Gustaf Olsson)
> > > > 5. Re: adding hydrogen to pdbqt ligand files (Eduardo Mayo)
> > > > 6. Amber20 Performance on RTX (Turing): known problems, with a
> > > > patch forthcoming (David Cerutti)
> > > > 7. questions for mdgx-virtual site (Gao J)
> > > > 8. Re: questions for mdgx-virtual site (David Cerutti)
> > > > 9. Re: questions for mdgx-virtual site (David Cerutti)
> > > > 10. igb for non-aqueous solvent? (Timothy Schutt)
> > > > 11. Re: cellulose chain (Pinky Mazumder)
> > > > 12. Re: Small molecules paramters (Gustavo Seabra)
> > > > 13. Re: cellulose chain (David A Case)
> > > >
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Thu, 28 May 2020 18:51:16 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] Amber20 pmemd.cuda installation and performance
> > > > problems
> > > > To: Thomas Zeiser <thomas.zeiser.fau.de>, AMBER Mailing List
> > > > <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAEmzWj108UxHJDdvTjuGJRyr=
> > > Tj7MOjSFL3a5F+GzJVRZ75ocQ.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > I have access to a machine in Darrin York's group that has a properly
> > > > situated RTX-2080Ti, and I have been able to benchmark the code and see
> > > the
> > > > performance hit (also, contrary to what I reported on another thread
> > > about
> > > > this, the Pascal GP100 is seeing a 5% DECREASE in performance, not an
> > > > increase with Amber20, so the problem is widespread). After further
> > > > consultation with Scott Legrand and one of our NVIDIA technical
> > > > collaborators, we have narrowed the problem to some things that are now
> > > > happening in the non-bonded kernels in order to protect us against
> > > > deprecations that NVIDIA plans to make in CUDA 11 and future releases.
> > > >
> > > > (Thomas, thank you for your efforts, but I think we have already solved
> > > the
> > > > problem, at least to the extent that testing on your platforms could
> > > inform
> > > > us. I may yet log in if we devise a fix and want to test it on a broad
> > > > array of RTX hardware, but that is an IF.)
> > > >
> > > > In particular, Scott and I looked over the kernel register spills, and
> > > > Amber20 is overall better in this regard than Amber18, although neither
> > > > code has a performance problem in this respect. Scott has also checked
> > > in
> > > > some safer, hardware-specific kernel launch bounds and these will be
> > > > applied in a future patch, but what is there is not causing a performance
> > > > problem nor, that we can tell, creating any other issue. Some users, and
> > > > even NVIDIA technicians themselves, have brought up possible performance
> > > > drag resulting from the cmake installation as opposed to the legacy
> > > build,
> > > > but I compiled with the legacy build system and I still see a 15% hit on
> > > > RTX-2080Ti, so any impact of cmake is marginal.
> > > >
> > > > In summary, we have traced the performance hit to two kernels, and
> > > > unfortunately they are the most time-consuming kernels in most MD
> > > > applications. While I am still trying to understand the degree that each
> > > > of the necessary changes contributes to the slowdown, the changes are not
> > > > things we can simply revert, and I do not know whether even a major
> > > > overhaul of the non-bonded kernel could mitigate the new CUDA calls that
> > > > will be required in all code going forward. Furthermore, two years ago I
> > > > attempted a major rewrite of the non-bonded routine. After climbing that
> > > > mountain and reaching over the last rock, I looked down to see that the
> > > > code was going to become much more complex, many niche features would
> > > have
> > > > been affected, and that while it might be nice for directions I would
> > > like
> > > > to see MD go, the new method was not a performance win across the board.
> > > >
> > > > I wish I came with better news, but it appears that this slowdown in
> > > > Amber20 is about where CUDA is going, not the result of any mistakes we
> > > > have made. We may be able to macro-out some of the calls for
> > > compilations
> > > > to recover a few percent on legacy chips like Pascal, and the Volta
> > > > architecture (V100 and Titan-V) seems to be resilient in the face of the
> > > > added synchronization calls. However, it looks like the Turing
> > > > architecture performance is going to suffer for the foreseeable future.
> > > > The hope I can offer is that the Ampere chips on the horizon appear to
> > > > resume an upward trend in the compute capacity of a single card, so in
> > > time
> > > > simulations will again start to get faster.
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Thu, May 28, 2020 at 2:26 PM Thomas Zeiser <thomas.zeiser.fau.de>
> > > wrote:
> > > >
> > > > > On Wed, May 27, 2020 at 08:35:38PM +0200, Thomas Zeiser wrote:
> > > > > > Hi Dave,
> > > > > >
> > > > > > please send me your SSH public key. I'll come back tomorrow with
> > > > > > further instructions.
> > > > >
> > > > > you have to connect with SSH as w17p0001 to port 22622 of
> > > > > grid.rrze.uni-erlangen.de
> > > > > e.g. ssh -4 -p 22622 w17p0001.grid.rrze.uni-erlangen.de
> > > > >
> > > > > That should give you a shell on "testfront1". There, you can use e.g.
> > > > > srun -w medusa --time=10:0:0 --pty /bin/bash
> > > > > to get an interactive job on the node "medusa" which hosts the GPUs.
> > > > >
> > > > > CUDA, etc. are only installed on "medusa". Both testfront1 and
> > > > > medusa can directly access data from the internet (through NAT).
> > > > >
> > > > > While you have a job running on medua, you can also SSH to medusa.
> > > > > Once the job ends, all procces are kill. Thus, if you want to use
> > > > > "screen", run it on testfront1.
> > > > >
> > > > > $HOME has a quota of 10 GB; $WORK of 333 GB.
> > > > >
> > > > >
> > > > > Best
> > > > >
> > > > > thomas
> > > > >
> > > > > > Best
> > > > > >
> > > > > > thomas
> > > > > >
> > > > > > On Wed, May 27, 2020 at 02:29:58PM -0400, David Cerutti wrote:
> > > > > > > This sounds like a great plan. I am about to test amber18 and
> > > amber20
> > > > > on a
> > > > > > > local machine in another lab. If I can get access to the server
> > > with a
> > > > > > > range of different Turing GPUs I can start to look at how your
> > > problem
> > > > > > > takes place.
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > Dave
> > > > > > >
> > > > > > >
> > > > > > > On Wed, May 27, 2020 at 9:08 AM Thomas Zeiser <
> > > thomas.zeiser.fau.de>
> > > > > wrote:
> > > > > > >
> > > > > > > > Hi Dave,
> > > > > > > >
> > > > > > > > On Wed, May 27, 2020 at 07:54:32AM -0400, David Cerutti wrote:
> > > > > > > > > I cannot make a meaningful test on an RTX-2080Ti because the
> > > card
> > > > > I have
> > > > > > > > > access to are not sufficiently powered to give the right
> > > numbers.
> > > > > I see
> > > > > > > > > about a 20% degradation relative to what Ross was able to get.
> > > > > Ditto for
> > > > > > > > > an RTX-6000, which is nearly as fast as a V100 despite having
> > > 20%
> > > > > too
> > > > > > > > > little power feeding it.
> > > > > > > >
> > > > > > > > we could provide you temporary access to our HPC systems to
> > > support
> > > > > > > > you in investigating the prossible performance degradation.
> > > > > > > >
> > > > > > > > I'd could either offer one host with four different Turing-based
> > > > > > > > GPUs (Geforce 2070 Super, 2080 Super, Quadro RTX 5000, and 6000)
> > > or
> > > > > > > > a node with 4x Geforce 2080Ti.
> > > > > > > >
> > > > > > > > Both systems are running Ubuntu 18.04. Cuda toolkits 9.0 up to
> > > 10.2
> > > > > > > > are installedi together with driver 440.64.00. Persistence-Mode
> > > is
> > > > > > > > enabled on all GPUs. cmake/3.11.1 would also be available as
> > > > > > > > module.
> > > > > > > >
> > > > > > > >
> > > > > > > > Best
> > > > > > > >
> > > > > > > > thomas
> > > > > > > >
> > > > > > > > > Dave
> > > > > > > > --
> > > > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > > > thomas.zeiser.fau.de
> > > > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > > > >
> > > > > >
> > > > > > --
> > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > thomas.zeiser.fau.de
> > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > >
> > > > > --
> > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > thomas.zeiser.fau.de
> > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Thu, 28 May 2020 21:33:01 -0400
> > > > From: David A Case <david.case.rutgers.edu>
> > > > Subject: Re: [AMBER] Simulating pyridine in water TIP3P
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > > 20200529013301.ljprvlrh2piy3nob.vpn-client-172-16-9-226.rutgers.edu>
> > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > >
> > > > On Thu, May 28, 2020, Debarati DasGupta wrote:
> > > >
> > > > >I faced this error in equilibration step. Should I have a smaller cut
> > > value?
> > > > >Cutoff list exceeds largest sphere in unit cell!!
> > > >
> > > > No: you need to have a bigger system. When a side of the periodic box
> > > > gets to be less than about 20 Ang., it gets to be too small for Amber to
> > > > handle, since Amber was designed and optimized for larger periodic
> > > > cells.
> > > >
> > > > You may be able to get away with setting skinnb to 1 (instead of its
> > > > default value of 2). That will allow you to go to slightly smaller
> > > > boxes. But it would be rather dangerous to reduce the cutoff value to
> > > > anything below 8 Ang: we cut off Lennard-Jones interactions at "cut",
> > > > and 8 Ang. is already on the edge of being to small.
> > > >
> > > > By far the simplest fix is to just use more water molecules in your
> > > > original setup.
> > > >
> > > > ....dac
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Thu, 28 May 2020 23:57:59 -0400
> > > > From: Kenneth Huang <kennethneltharion.gmail.com>
> > > > Subject: Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory?
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > > CALeh7kALqvra6YccT-Sp4J7sMPJA37ArLhizviAkuUHjsEdrxw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi Christina,
> > > >
> > > > Thanks a lot for the insight and script! That more or less covers for
> > > what
> > > > I wanted to do NOE and CSP wise, and LAMORD should more or less fill in
> > > the
> > > > gap that the protein CSP softwares I found weren't able to do.
> > > >
> > > > Best,
> > > >
> > > > Kenneth
> > > >
> > > > On Thu, May 28, 2020 at 8:42 AM Christina Bergonzo <cbergonzo.gmail.com>
> > > > wrote:
> > > >
> > > > > Hi Kenneth,
> > > > >
> > > > > I do not know of any stand alone tools that will calculate NMR
> > > observables
> > > > > from a trajectory.
> > > > > I regularly do this without too much hassle using a combination of
> > > bash/awk
> > > > > scripting and Cpptraj/shifts.
> > > > > I also back out NOE distances from distance restraints - if you want to
> > > > > predict NOEs using a trajectory, that's a different question (see
> > > Henriksen
> > > > > et al. JPCB, dx.doi.org/10.1021/jp400530e), but also distance based.
> > > > >
> > > > > If you look at the Cpptraj distance command, there is an option for
> > > > > evaluating a distance as an NOE.
> > > > > I write a script that takes my atoms of interest from whatever
> > > experimental
> > > > > file format I have, and formats them into the distance command:
> > > > >
> > > > > distance d0 :1.H1' :1.H4' type noe bound 0.0 bound 7.0 out
> > > > > dist/noe.val.0.dat
> > > > > ....
> > > > > distance d50 :6.H5'' :6.H6 type noe bound 0.0 bound 7.0 out
> > > > > dist/noe.val.50.dat
> > > > > analyze statistics all out noe.dat
> > > > >
> > > > > The last part dumps analysis of each distance into a file (noe.dat)
> > > > > containing initial and final values, avg and standard deviation, 1/r^6
> > > > > averages, # of violations, etc.
> > > > > Example output:
> > > > >
> > > > > STATISTICS :1.H1' and :1.H4'
> > > > > AVERAGE: 3.0492 (0.2559 stddev)
> > > > > INITIAL: 3.0944
> > > > > FINAL: 3.2662
> > > > > NOE SERIES: S < 2.9, M < 3.5, W < 5.0, blank otherwise.
> > > > > |SMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM|
> > > > > NOE < 7.00 for 100.00% of the time
> > > > > NOE <r^-6>^(-1/6)= 2.9650
> > > > > #Violations: Low= 0 High= 0 Total= 0
> > > > > Rexp= 7.0000 <Violation>= -4.0350
> > > > >
> > > > > < 2.5 2.5-3.5 3.5-4.5 4.5-5.5 5.5-6.5 > 6.5
> > > > > -------------------------------------------------------
> > > > > %occupied | 2.4 | 95.1 | 2.5 | | | |
> > > > > average | 2.402 | 3.051 | 3.611 | | | |
> > > > > stddev | 0.084 | 0.223 | 0.103 | | | |
> > > > > -------------------------------------------------------
> > > > > __________________________________________________________________
> > > > >
> > > > > For chemical shifts for nucleic acids, I use shifts for protons, and
> > > > > there's larmor-D for proton and carbon shifts.
> > > > > And, I go through a similar procedure, where I look at the experiment
> > > to
> > > > > see what's be deposited, use shifts to calculate those values from
> > > PDBs (I
> > > > > have found you'll need to rename 5' and 3' ends to their non-terminal
> > > > > counterparts i.e., C3 to C), and then calculate for each frame and
> > > average.
> > > > >
> > > > > Good luck!
> > > > > -Christina
> > > > >
> > > > > On Wed, May 27, 2020 at 7:48 PM Kenneth Huang <
> > > kennethneltharion.gmail.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > A general question- does anyone know of tools (assuming there isn't a
> > > > > > combined suite) for calculating CSP or NOEs from a trajectory? I know
> > > > > > there's SPARTA+ and shiftX2 for protein CSPs for proteins, but with
> > > DNA
> > > > > all
> > > > > > I've seen is the NMR option in Gaussian, which seems prohibitively
> > > > > > expensive.
> > > > > >
> > > > > > Likewise for NOEs I know of MD2NOE but haven't ever used it in
> > > context of
> > > > > > DNA, and other than back-calculating from the distance restraints, I
> > > was
> > > > > > just wondering if there had been any other options in cpptraj?
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Kenneth
> > > > > > --
> > > > > > Ask yourselves, all of you, what power would hell have if those
> > > > > imprisoned
> > > > > > here could not dream of heaven?
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > -----------------------------------------------------------------
> > > > > Christina Bergonzo
> > > > > Research Chemist
> > > > > Biomolecular Measurement Division, MML, NIST
> > > > > -----------------------------------------------------------------
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Ask yourselves, all of you, what power would hell have if those
> > > imprisoned
> > > > here could not dream of heaven?
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 4
> > > > Date: Fri, 29 May 2020 05:53:03 +0000
> > > > From: Gustaf Olsson <gustaf.olsson.lnu.se>
> > > > Subject: Re: [AMBER] Small molecules paramters
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID: <EDDA8042-177F-409D-9875-76E4A5AA9EF2.lnu.se>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > According to the fifth information webpage
> > > >
> > > > ?Amber-compatible parameters can also be generated, although Amber-style
> > > force field files are not output (users can convert though with parmed)?
> > > > - http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> > > >
> > > > It should be very possible. If it is advisable, I suspect that depends
> > > on the quality of generated parameters.
> > > >
> > > > Best regards
> > > > // Gustaf
> > > >
> > > >
> > > > On 28 May 2020, at 14:47, Athena N <athena.nas01.gmail.com<mailto:
> > > athena.nas01.gmail.com>> wrote:
> > > >
> > > > Hi all,
> > > >
> > > > I want to know if it advisable to use any other force fields than gaff
> > > for
> > > > small molecules like some indole and pyridine systems.? If we generate
> > > some
> > > > parameters using fftk (force field tool kit), could we use those and do
> > > the
> > > > simulation in AMBER?
> > > >
> > > > Thank you all
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 5
> > > > Date: Fri, 29 May 2020 02:25:00 -0400
> > > > From: Eduardo Mayo <eduardomayoyanes.gmail.com>
> > > > Subject: Re: [AMBER] adding hydrogen to pdbqt ligand files
> > > > To: amber.ambermd.org
> > > > Message-ID:
> > > > <CAFVrw=SeTENo9zGCZO3vHbQ=
> > > ruZGs8HFYVJNv6WYqY2yaMwxyw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi!
> > > > I recommend:
> > > > 1 convert to .mol file using babel (with and without -h) and check if the
> > > > tautomeric state is the desired.
> > > > 2 if 1 didn't work then covert to smarts or smiles( so if you got a
> > > > tautomeric state with local charge the smarts/smiles will have this
> > > > information) . Use rdkit to covert smiles/smarts to rdkit.Mol and add
> > > then
> > > > the hydrogen. Chem.Embedded the molecule so you have a 3D model. The read
> > > > the mol file using Chem.MolFromMolFile. Align (you may need find the
> > > mcse)
> > > > the molecule obtained from smiles to the molecule obtained from the mol
> > > > file.
> > > >
> > > >
> > > >
> > > >
> > > > Message: 3
> > > > Date: Tue, 28 Apr 2020 21:15:36 +0000 (UTC)
> > > > From: Marawan Hussien <marawanhussain.yahoo.com>
> > > > Subject: [AMBER] adding hydrogen to pdbqt ligand files
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID: <1174479232.1819345.1588108536730.mail.yahoo.com>
> > > > Content-Type: text/plain; charset=UTF-8
> > > >
> > > > Is there is a standard leap command to add hydrogen atoms to non-polar
> > > > atoms (carbons) only during system building? I am preparing a
> > > > protein-ligand system for MD from pdbqt protein-ligand complex and do not
> > > > want to change the ligand tautomeric state.? I tried rdkit, obabel,
> > > chimera
> > > > but every tool I tried will add hydrogen to the entire molecule, not
> > > carbon
> > > > atoms only? Any suggestion?
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 6
> > > > Date: Fri, 29 May 2020 02:30:20 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: [AMBER] Amber20 Performance on RTX (Turing): known problems,
> > > > with a patch forthcoming
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > > CAEmzWj2pfjPxJg0-O+th+VyMcBsjFhqERfM0AJDtxZAzps6v2Q.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Dear Users,
> > > >
> > > > As has been shared on this listserv, many users are finding that Amber20
> > > is
> > > > not as fast on Turing architectures for PME simulations as Amber18. The
> > > > source of this problem has now been identified, and indeed it affects
> > > much
> > > > more than just Turing, but the 15-20% slowdown seen on Turing is merely
> > > the
> > > > most severe case.
> > > >
> > > > The slowdown itself does NOT reflect any bugs or issues that would
> > > > necessitate repeating experiments. The problem, rather, is that some
> > > > future-proofing that our collaborators at NVIDIA kindly performed for us
> > > > has led to more GPU effort in synchronization. The benefit of this is
> > > > that, come CUDA 11 and the new Ampere chipset, pmemd.cuda is already
> > > > prepared to run on the cards (at a substantially greater speed than is
> > > > currently possible with a V100, which in my view competes with RTX-6000
> > > for
> > > > top dog). However, legacy chipsets that do not need to perform the
> > > > synchronization required for CUDA 11 to work properly will suffer in
> > > > performance.
> > > >
> > > > Contrary to what I warned yesterday afternoon, a fix is possible and we
> > > > already have it. A compiler-specific directive will create separate code
> > > > paths for the various chipsets and mask out the synchronization where it
> > > is
> > > > not needed, recovering the Amber18 performance while still keeping the
> > > code
> > > > in a state that is ready for the next architecture.
> > > >
> > > > I would like to thank Scott Legrand, Peng Wang, and others at NVIDIA who
> > > > contributed either to the future-proofing or the short-term recovery
> > > > effort. As you sit at home preparing your new simulations, please enjoy
> > > > some ice cream or other simple treat while you await the forthcoming
> > > patch
> > > > that will put Amber20 back where it should be on the benchmarks.
> > > >
> > > > Sincerely,
> > > >
> > > > Dave Cerutti
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 7
> > > > Date: Fri, 29 May 2020 16:29:44 +0800 (GMT+08:00)
> > > > From: "Gao J" <21919039.zju.edu.cn>
> > > > Subject: [AMBER] questions for mdgx-virtual site
> > > > To: amber.ambermd.org
> > > > Message-ID: <59110ff3.e289d.1725f8d21aa.Coremail.21919039.zju.edu.cn>
> > > > Content-Type: text/plain; charset=UTF-8
> > > >
> > > > Hello
> > > >
> > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > repulsions between themselves merely. My parameters for &rule were as
> > > follows and I got an error said "ReadEPRuleFile >> Error. Extra point name
> > > unspecified." So I wonder what the correct format of "epname" or "atom"
> > > required. What's more, I am a little confused if any parameters needed for
> > > "excl[1,2]".
> > > >
> > > > I really appreciate for your help!
> > > >
> > > > &rule
> > > >
> > > > frame[1,2]: C1 C4
> > > >
> > > > epname: VSB
> > > >
> > > > atom: VSB
> > > >
> > > > style: 1
> > > >
> > > > excl[1,2]
> > > >
> > > > v12: 0.5
> > > >
> > > > Sig: 21
> > > >
> > > > eps: 0.01
> > > >
> > > > residue: UNK
> > > >
> > > > &end
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 8
> > > > Date: Fri, 29 May 2020 05:42:42 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > > CAEmzWj1n-DX_UodrWv9srcjbPRDDb03vmabfuFwTo5Rau6SO3w.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > OK, so good evening! mdgx is not going to be FAST simulator but if you
> > > > just need to get a system running a few thousand (or even million) steps
> > > of
> > > > MD then it'll do fine. I am working right now to enable this virtual
> > > site
> > > > functionality in pmemd and also tleap, so with luck it'll be possible to
> > > > create more interesting molecular models in the standard MD engines soon.
> > > >
> > > > For the &rule namelist, it's... a &namelist, just like &cntrl or &ewald
> > > in
> > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > technically the Fortran standard, but it gets things pretty well and lets
> > > > you have some flexibility. I would try writing this first:
> > > >
> > > > &rule
> > > > frame1 = "C1",
> > > > frame2 = "C2",
> > > > epname = "VSB",
> > > > style = 1,
> > > > v12 = 0.5,
> > > > sig = 2.1,
> > > > eps = 0.05,
> > > > residue = "UNK",
> > > > &end
> > > >
> > > > In your input, you have lots of colon punctuation (:) that mdgx won't
> > > know
> > > > how to parse (nor will sander or pmemd). And I've written the above in
> > > > shorthand. There are aliases for all those keywords if you find one or
> > > the
> > > > other easier to remember ("sig" can also be "Sigma"), but the keywords
> > > ARE
> > > > case-sensitive. The "epname" keyword actually has four aliases,
> > > "epname",
> > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard there.)
> > > >
> > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > points: if they're right on the middle of a bond, or equally close to
> > > more
> > > > than one real atom in general, how do we count their exclusions? (This
> > > is a
> > > > reason that one of the experienced force field developers I work with
> > > > demands that all of these extra points be close to their ONE parent atom
> > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > definition, an extra point is 1:1 to its parent atom, so all non-bonded
> > > > exclusions of the frame1 atom will be inherited by the extra point. But
> > > if
> > > > you specify excl2, it's going to take your frame2 atom and say that the
> > > > extra point is also 1:1 to that. Ditto for excl3, so the extra point is
> > > > accumulating more and more exclusions, atoms that it will not count
> > > > interactions with.
> > > >
> > > > This makes me realize that I need to document this part of the code a bit
> > > > better, specifically in the onboard manual. There are descriptions for
> > > all
> > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command
> > > line.
> > > > But not for &rule...
> > > >
> > > > Happy to help more, and you are not the first to make use of mdgx to
> > > create
> > > > some very unorthodox (not unusual, just not what the typical programs
> > > > simulate) molecular models. It HAS been done before, and not just by me
> > > :-)
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > >
> > > > > Hello
> > > > >
> > > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > > repulsions between themselves merely. My parameters for &rule were as
> > > > > follows and I got an error said "ReadEPRuleFile >> Error. Extra point
> > > name
> > > > > unspecified." So I wonder what the correct format of "epname" or "atom"
> > > > > required. What's more, I am a little confused if any parameters needed
> > > for
> > > > > "excl[1,2]".
> > > > >
> > > > > I really appreciate for your help!
> > > > >
> > > > > &rule
> > > > >
> > > > > frame[1,2]: C1 C4
> > > > >
> > > > > epname: VSB
> > > > >
> > > > > atom: VSB
> > > > >
> > > > > style: 1
> > > > >
> > > > > excl[1,2]
> > > > >
> > > > > v12: 0.5
> > > > >
> > > > > Sig: 21
> > > > >
> > > > > eps: 0.01
> > > > >
> > > > > residue: UNK
> > > > >
> > > > > &end
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 9
> > > > Date: Fri, 29 May 2020 05:49:46 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAEmzWj3n5=
> > > jWdmadVwoi-DVsCWC90bGnhNQ7440eWsoDWEPLnQ.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Another note: if you are trying to simulate a mixture of two solvents and
> > > > finding that the two molecular models do not want to stay mixed, this is
> > > a
> > > > well-known problem in many models. If you want to just have virtual
> > > sites
> > > > (extra points) sticking out of the benzene to push benzenes away from
> > > each
> > > > other, that's one way to do it but it sounds extremely "staged" shall we
> > > > say. It would be like you've contrived the model and getting any useful
> > > > properties out of it would be a hard sell. I'm not actually sure you
> > > could
> > > > do this--mdgx is going to see the LJ parameters you assign to the virtual
> > > > sites and then try to apply the reigning LJ combining rule to determine
> > > how
> > > > they interact with other atoms. So they'd interact with ALL other atoms
> > > of
> > > > the simulation according to Lorentz-Berthelot combining rules, I expect,
> > > > not just other virtual sites.
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Fri, May 29, 2020 at 5:42 AM David Cerutti <dscerutti.gmail.com>
> > > wrote:
> > > >
> > > > > OK, so good evening! mdgx is not going to be FAST simulator but if you
> > > > > just need to get a system running a few thousand (or even million)
> > > steps of
> > > > > MD then it'll do fine. I am working right now to enable this virtual
> > > site
> > > > > functionality in pmemd and also tleap, so with luck it'll be possible
> > > to
> > > > > create more interesting molecular models in the standard MD engines
> > > soon.
> > > > >
> > > > > For the &rule namelist, it's... a &namelist, just like &cntrl or
> > > &ewald in
> > > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > > technically the Fortran standard, but it gets things pretty well and
> > > lets
> > > > > you have some flexibility. I would try writing this first:
> > > > >
> > > > > &rule
> > > > > frame1 = "C1",
> > > > > frame2 = "C2",
> > > > > epname = "VSB",
> > > > > style = 1,
> > > > > v12 = 0.5,
> > > > > sig = 2.1,
> > > > > eps = 0.05,
> > > > > residue = "UNK",
> > > > > &end
> > > > >
> > > > > In your input, you have lots of colon punctuation (:) that mdgx won't
> > > know
> > > > > how to parse (nor will sander or pmemd). And I've written the above in
> > > > > shorthand. There are aliases for all those keywords if you find one
> > > or the
> > > > > other easier to remember ("sig" can also be "Sigma"), but the keywords
> > > ARE
> > > > > case-sensitive. The "epname" keyword actually has four aliases,
> > > "epname",
> > > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard
> > > there.)
> > > > >
> > > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > > points: if they're right on the middle of a bond, or equally close to
> > > more
> > > > > than one real atom in general, how do we count their exclusions? (This
> > > is a
> > > > > reason that one of the experienced force field developers I work with
> > > > > demands that all of these extra points be close to their ONE parent
> > > atom
> > > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > > definition, an extra point is 1:1 to its parent atom, so all non-bonded
> > > > > exclusions of the frame1 atom will be inherited by the extra point.
> > > But if
> > > > > you specify excl2, it's going to take your frame2 atom and say that the
> > > > > extra point is also 1:1 to that. Ditto for excl3, so the extra point
> > > is
> > > > > accumulating more and more exclusions, atoms that it will not count
> > > > > interactions with.
> > > > >
> > > > > This makes me realize that I need to document this part of the code a
> > > bit
> > > > > better, specifically in the onboard manual. There are descriptions
> > > for all
> > > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command
> > > line.
> > > > > But not for &rule...
> > > > >
> > > > > Happy to help more, and you are not the first to make use of mdgx to
> > > > > create some very unorthodox (not unusual, just not what the typical
> > > > > programs simulate) molecular models. It HAS been done before, and not
> > > just
> > > > > by me :-)
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > > >
> > > > >> Hello
> > > > >>
> > > > >> I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > >> ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > >> repulsions between themselves merely. My parameters for &rule were as
> > > > >> follows and I got an error said "ReadEPRuleFile >> Error. Extra
> > > point name
> > > > >> unspecified." So I wonder what the correct format of "epname" or
> > > "atom"
> > > > >> required. What's more, I am a little confused if any parameters
> > > needed for
> > > > >> "excl[1,2]".
> > > > >>
> > > > >> I really appreciate for your help!
> > > > >>
> > > > >> &rule
> > > > >>
> > > > >> frame[1,2]: C1 C4
> > > > >>
> > > > >> epname: VSB
> > > > >>
> > > > >> atom: VSB
> > > > >>
> > > > >> style: 1
> > > > >>
> > > > >> excl[1,2]
> > > > >>
> > > > >> v12: 0.5
> > > > >>
> > > > >> Sig: 21
> > > > >>
> > > > >> eps: 0.01
> > > > >>
> > > > >> residue: UNK
> > > > >>
> > > > >> &end
> > > > >>
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> AMBER.ambermd.org
> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 10
> > > > Date: Fri, 29 May 2020 08:40:59 -0500
> > > > From: Timothy Schutt <tschutt7.gmail.com>
> > > > Subject: [AMBER] igb for non-aqueous solvent?
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAGGi8+gfyC=aCWfrDO+8oEpWCOzyTBnGQqUja4yv=
> > > 9w1o2Bm5A.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi Amber Folks!
> > > >
> > > > Is it an okay approximation to use igb=1 and extdiel=*dielectric value*
> > > to
> > > > represent a non-aqueous solvent implicitly?
> > > >
> > > > I would like to investigate some surface binding interactions of a
> > > > non-aqueous solvent but the solvents are too viscous to get decent
> > > sampling
> > > > in a reasonable time frame so my thought was to use 2D umbrella sampling
> > > > across the surface sites using just one explicit solvent molecule with
> > > the
> > > > rest being implicit. In each solvent system I would use the different one
> > > > explicit solvent and the approrpiate external dielectric for that solvent
> > > > in bulk. Would that be an accurate enough approach to provide reliable
> > > > trends of mapping different solvents interactions with the surface?
> > > >
> > > > Any advice is greatly appreciated, Thanks!
> > > >
> > > > -Tim
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 11
> > > > Date: Fri, 29 May 2020 09:46:58 -0500
> > > > From: Pinky Mazumder <pmazumder67.gmail.com>
> > > > Subject: Re: [AMBER] cellulose chain
> > > > To: AMBER Mailing List <amber.ambermd.org>, Lachele Foley
> > > > <lf.list.gmail.com>
> > > > Message-ID:
> > > > <
> > > CAFoDHbjw9EqX4ewswc+agnru_2pRMZR2kssyXzUjW0u5x7GRQw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Thank you.
> > > >
> > > > I can place the chains parallel to each other. After that, I need to see
> > > > the h-bond interaction between the polymers. For that I ran the
> > > simulations
> > > > with energy minimization, heating and production MD.
> > > >
> > > > Even after, I do not see the H-Bond. To do so, what process I need to
> > > > follow?
> > > >
> > > > Thank you.
> > > >
> > > > Sincerely,
> > > > Pinky
> > > >
> > > > On Sat, May 16, 2020 at 4:33 AM Lachele Foley <lf.list.gmail.com> wrote:
> > > >
> > > > > When you copy the chains, they have exactly the same x,y,z
> > > > > coordinates. In other words, they are right on top of each other.
> > > > >
> > > > > You will need to use the translate and/or transpose commands to put
> > > > > them into the proper relative geometries.
> > > > >
> > > > > On Fri, May 15, 2020 at 11:53 PM Pinky Mazumder <pmazumder67.gmail.com
> > > >
> > > > > wrote:
> > > > > >
> > > > > > Please discard my previous message.
> > > > > >
> > > > > >
> > > > > > Thank you so much for your cordial response.
> > > > > >
> > > > > >
> > > > > > I can copy the chain using this command and the numbers of atoms are
> > > > > > increasing.
> > > > > >
> > > > > >
> > > > > > However, I am not able to see the two chains together in vmd or in
> > > the
> > > > > > xleap using the edit command.
> > > > > >
> > > > > >
> > > > > > Could you please help me in this regard?
> > > > > >
> > > > > >
> > > > > > Thank you again.
> > > > > >
> > > > > > Sincerely,
> > > > > > Pinky
> > > > > >
> > > > > > On Fri, May 15, 2020 at 10:51 PM Pinky Mazumder <
> > > pmazumder67.gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Thank you so much for your cordial response.
> > > > > > >
> > > > > > >
> > > > > > > But, I can show the two chains together using vmd. I can copying
> > > the
> > > > > chain
> > > > > > > because the numbers of atoms are increasing.
> > > > > > >
> > > > > > >
> > > > > > > However, I am not able to see the two chains together.
> > > > > > >
> > > > > > >
> > > > > > > Could you please help me in this regard?
> > > > > > >
> > > > > > >
> > > > > > > Thank you again.
> > > > > > >
> > > > > > > Sincerely,
> > > > > > >
> > > > > > > On Fri, May 15, 2020 at 10:09 PM Lachele Foley <lf.list.gmail.com>
> > > > > wrote:
> > > > > > >
> > > > > > >> First, you need to know the geometric relationships between the
> > > > > > >> chains. The relationships will differ based on the source of the
> > > > > > >> cellulose.
> > > > > > >>
> > > > > > >> In leap, you can use:
> > > > > > >>
> > > > > > >> chain2 = copy chain1
> > > > > > >>
> > > > > > >> to make a copy of a chain.
> > > > > > >>
> > > > > > >> Then, once you know the relative geometries, you can use translate
> > > > > > >> and/or transform to position the chains properly with respect to
> > > each
> > > > > > >> other.
> > > > > > >>
> > > > > > >> Alternatively, find an experimentally-determined structure, such
> > > as an
> > > > > > >> X-ray or cryo-EM structure.
> > > > > > >>
> > > > > > >> Also consider contacting Dr. Jodi Hadden. She can probably help
> > > you,
> > > > > > >> but she's pretty busy with other stuff, so you might have to be
> > > > > > >> patient.
> > > > > > >>
> > > > > > >> On Fri, May 15, 2020 at 1:01 PM Pinky Mazumder <
> > > pmazumder67.gmail.com
> > > > > >
> > > > > > >> wrote:
> > > > > > >> >
> > > > > > >> > Hi David,
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Thank you for your response.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > I have been able to make the polymer of cellulose. But I need
> > > > > multiple
> > > > > > >> > chains together.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Could you please suggest how can I replicate the same polymer
> > > chain
> > > > > or
> > > > > > >> can
> > > > > > >> > I build the multiple number of polymer chain together?
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Is there any specific tutorial or command that I need to follow?
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Thank you.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Kind regards,
> > > > > > >> >
> > > > > > >> > Pinky
> > > > > > >> >
> > > > > > >> > On Sun, Apr 5, 2020, 12:20 PM David A Case <
> > > david.case.rutgers.edu>
> > > > > > >> wrote:
> > > > > > >> >
> > > > > > >> > > On Thu, Apr 02, 2020, Pinky Mazumder wrote:
> > > > > > >> > > >
> > > > > > >> > > >I want to build a chain of cellulose. So when I am trying to
> > > do
> > > > > this
> > > > > > >> by
> > > > > > >> > > >using foo sequence command.
> > > > > > >> > > >
> > > > > > >> > > > It says that '' Error : sequence : ILLEGAL UNIT named Glc''.
> > > > > > >> > >
> > > > > > >> > > Are you inside tleap at this point? If so, execute the "list"
> > > > > > >> command,
> > > > > > >> > > and see if Glc is one of the units listed. If not, you would
> > > > > need to
> > > > > > >> > > somehow load the units you want.
> > > > > > >> > >
> > > > > > >> > > Carbohydrates are discussed in Chap. 3 of the Amber Reference
> > > > > Manual:
> > > > > > >> > > you might see if that would help.
> > > > > > >> > >
> > > > > > >> > > If this is not a tleap error, then please give more details
> > > about
> > > > > > >> > > exactly what you mean by "using foo sequence command".
> > > > > > >> > >
> > > > > > >> > > ...thx...dac
> > > > > > >> > >
> > > > > > >> > >
> > > > > > >> > > _______________________________________________
> > > > > > >> > > AMBER mailing list
> > > > > > >> > > AMBER.ambermd.org
> > > > > > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >> > >
> > > > > > >> > _______________________________________________
> > > > > > >> > AMBER mailing list
> > > > > > >> > AMBER.ambermd.org
> > > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >> --
> > > > > > >> :-) Lachele
> > > > > > >> Lachele Foley
> > > > > > >> CCRC/UGA
> > > > > > >> Athens, GA USA
> > > > > > >>
> > > > > > >> _______________________________________________
> > > > > > >> AMBER mailing list
> > > > > > >> AMBER.ambermd.org
> > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Pinky, Sharmi
> > > > > > > AL,US
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Pinky, Sharmi
> > > > > > AL,US
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > :-) Lachele
> > > > > Lachele Foley
> > > > > CCRC/UGA
> > > > > Athens, GA USA
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Pinky, Sharmi
> > > > AL,US
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 12
> > > > Date: Fri, 29 May 2020 12:20:56 -0400
> > > > From: Gustavo Seabra <gustavo.seabra.gmail.com>
> > > > Subject: Re: [AMBER] Small molecules paramters
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAO4guEKk=
> > > 2u1gnzrdBp8hSCDsV5yaN2Q52Muip+SW3_QcOW_hg.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Although it is possible to convert parameters to AMBER *format*, so they
> > > > can be read by AMBER, this is not the ideal. Bear in mind that the MD
> > > force
> > > > fields rely on a fine balance between charges and force constants
> > > > obtained from multiple calculations, and that each force field "flavor"
> > > > uses a different methodology to obtain those parameters. So, ideally, you
> > > > will want to use for your small molecule the same methodology that was
> > > used
> > > > to derive parameters for the rest of the system, or at least have some
> > > > indication that the parameters are compatible. GAFF (ad GAFF2) have been
> > > > developed with that in mind, so their parameters are, in principle,
> > > > compatible with the Amber force fields. If you get the parameters from
> > > > other sources, make sure you do some extra testing.
> > > >
> > > > All the best,
> > > > --
> > > > Gustavo Seabra.
> > > >
> > > >
> > > > On Thu, May 28, 2020 at 8:47 AM Athena N <athena.nas01.gmail.com> wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I want to know if it advisable to use any other force fields than gaff
> > > for
> > > > > small molecules like some indole and pyridine systems.? If we generate
> > > some
> > > > > parameters using fftk (force field tool kit), could we use those and
> > > do the
> > > > > simulation in AMBER?
> > > > >
> > > > > Thank you all
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 13
> > > > Date: Fri, 29 May 2020 12:32:06 -0400
> > > > From: David A Case <david.case.rutgers.edu>
> > > > Subject: Re: [AMBER] cellulose chain
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > > 20200529163206.k2wr3wlvv2kcwtee.vpn-client-172-16-9-226.rutgers.edu>
> > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > >
> > > > On Fri, May 29, 2020, Pinky Mazumder wrote:
> > > > >
> > > > >I can place the chains parallel to each other. After that, I need to see
> > > > >the h-bond interaction between the polymers. For that I ran the
> > > simulations
> > > > >with energy minimization, heating and production MD.
> > > > >
> > > > >Even after, I do not see the H-Bond. To do so, what process I need to
> > > > >follow?
> > > >
> > > > I guessing you need a better starting structure. Do the chains move
> > > > much during the simulation? If there are no inter-chain hydrogen bonds
> > > > in the starting structure, it may difficult to get them to form just
> > > > with MD, even if the H-bonded structure has a lower free energy.
> > > >
> > > > You may be able to get some good ideas, plus a feeling for how mobile
> > > > your chains are, by looking at the trajectories you have. Generally, MD
> > > > simluations sample configurations close to the starting point, and
> > > > either long simulations or advanced sampling methods are required to
> > > > find quite different structures.
> > > >
> > > > If you know what H-bonds you would like to form, you could add
> > > > restraints (called "NMR" restraints in Amber lingo, for historical
> > > > reasons) that will pull the H-bond donor and acceptor atoms to an
> > > > H-bonding geometry.
> > > >
> > > > ....good luck...dac
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > > End of AMBER Digest, Vol 3017, Issue 1
> > > > **************************************
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > End of AMBER Digest, Vol 3019, Issue 1
> > **************************************
>
> ------------------------------
>
> Message: 4
> Date: Mon, 1 Jun 2020 06:28:03 -0400
> From: David Cerutti <dscerutti.gmail.com>
> Subject: Re: [AMBER] AMBER Digest, Vol 3019, Issue 1
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEmzWj0psvRYoFx4VXdw8HyFi=2VQpmTccy-+ASh6S7Sh1YKcQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> What you need to realize is that:
> - Frame atom 1 has some 1:2, 1:3, and 1:4 exclusions. The extra point will
> ALWAYS inherit these.
> - Frame atom 2 has its own 1:2, 1:3, and 1:4 exclusions. If you specify
> excl2, the exclusions of frame atom 2 will also become exclusions of the
> extra point.
> - Frame atom 3, same thing.
>
> So, by including excl2 = 1 or excl3 = 1 (and that is, 1 = TRUE in this
> syntax), you ware expanding the array of atoms that the extra point will
> see as exclusions. You are calling for it to exclude frame atom 2, but
> that has probably already been done as frame atom 2 is usually bonded to
> frame atom 1 anyway. Instead, you are giving the extra point a lot more
> atoms to consider exclusions.
>
> Dave
>
>
> Dave
>
>
> On Sun, May 31, 2020 at 10:05 PM Gao J <21919039.zju.edu.cn> wrote:
>
> > Hi Dave:
> > I am confused of some distinctions between your suggestion and Amber
> > Manual.
> > I think "But if you specify excl2, it's going to take your frame2 atom and
> > say that the extra point is also 1:1 to that." means the virtual sites will
> > inherit the interactions of the atom I have excluded.
> > While in the Amber Manual, the explanation of excl[2,3] is that "The
> > virtual site is definitively 1:1 bound to frame atom 1 and thereby inherits
> > all 1:2, 1:3, and 1:4 neighbors of frame atom 1, but if ? is 2 or 3 then
> > the virtual site will also be considered 1:1 to frame atoms 2 or 3 and
> > inherit their bonded neighbors as well. This will not affect the 1:2, 1:3,
> > and 1:4 neighbor lists of the frame atoms themselves." which I think the
> > virtual sites will inherit the inherit the interactions except the atom I
> > have excluded(is "?" the atom not in the excl list?). I don't know whether
> > this problem comes from my improper understanding or the misinterpretation
> > of the Manual.(T?T)
> > Thank you once again!
> >
> > Best
> > Gao J
> >
> > > -----????-----
> > > ???: amber-request.ambermd.org
> > > ????: 2020-06-01 03:00:01 (???)
> > > ???: amber.ambermd.org
> > > ??:
> > > ??: AMBER Digest, Vol 3019, Issue 1
> > >
> > > Send AMBER mailing list submissions to
> > > amber.ambermd.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > or, via email, send a message with subject or body 'help' to
> > > amber-request.ambermd.org
> > >
> > > You can reach the person managing the list at
> > > amber-owner.ambermd.org
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of AMBER digest..."
> > >
> > >
> > > AMBER Mailing List Digest
> > >
> > > Today's Topics:
> > >
> > > 1. Re: AMBER Digest, Vol 3017, Issue 1 (Gao J)
> > > 2. amber20 output header (Baker, Joseph)
> > > 3. Re: amber20 output header (David Cerutti)
> > > 4. Re: AMBER Digest, Vol 3017, Issue 1 (David Cerutti)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Sun, 31 May 2020 10:18:36 +0800 (GMT+08:00)
> > > From: "Gao J" <21919039.zju.edu.cn>
> > > Subject: Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
> > > To: amber.ambermd.org
> > > Message-ID: <1f7ca382.e1ef4.1726886121b.Coremail.21919039.zju.edu.cn>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Hi Dave:
> > > It's so kind of you to help me.
> > > I modified my &rule file for a tentative short heating simulation of a
> > minimized system, while "mdgx.MPI" neither returned any output nor exited
> > with an error for a long time. The only message which seems nonlethal was
> > that "Netcdf restart min3.rst does not ave velocity info, Warning:No
> > velocities in restart, setting all to 0.0". I had set "irest=0" but no
> > randam velocities assigned. Could you please have a check for what's going
> > wrong?
> > > As for your note about the interactions between virtual sites and real
> > atoms, what if I exclude both frame1 and frame2 to keep the virtual sites
> > out of any nonbonded interaction with real atoms? I am a newcomer of Amber
> > and not sure if the combining rule would take these sites into
> > consideration in this circumstance.
> > > Thanks a lot for your gudiance!
> > > Best
> > > Gao J
> > >
> > > my input file:
> > > &files
> > > -p compw.prmtop
> > > -c min3.rst
> > > -xpt rule.in
> > > -o eq1.out
> > > -r eq1.rst
> > > -x eq1.mdcrd
> > > &end
> > > &cntrl
> > > imin=0,
> > irest=0,nstlim=1000,dt=0.002,cut=8.0,ntb=1,ntpr=500,ntwx=500,ntt=3,gamma_ln=2.0,
> > > tempi=0.0,temp0=300.0,ioutfm=1,
> > > &end
> > > my &rule file:
> > > &rule
> > > frame1="C1", frame2="C4", epname="VSB", style=1, excl1, v12=0.5,
> > sig=2.1, eps=0.05, residue="UNK",
> > > &end
> > >
> > > > -----????-----
> > > > ???: amber-request.ambermd.org
> > > > ????: 2020-05-30 03:00:01 (???)
> > > > ???: amber.ambermd.org
> > > > ??:
> > > > ??: AMBER Digest, Vol 3017, Issue 1
> > > >
> > > > Send AMBER mailing list submissions to
> > > > amber.ambermd.org
> > > >
> > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > or, via email, send a message with subject or body 'help' to
> > > > amber-request.ambermd.org
> > > >
> > > > You can reach the person managing the list at
> > > > amber-owner.ambermd.org
> > > >
> > > > When replying, please edit your Subject line so it is more specific
> > > > than "Re: Contents of AMBER digest..."
> > > >
> > > >
> > > > AMBER Mailing List Digest
> > > >
> > > > Today's Topics:
> > > >
> > > > 1. Re: Amber20 pmemd.cuda installation and performance problems
> > > > (David Cerutti)
> > > > 2. Re: Simulating pyridine in water TIP3P (David A Case)
> > > > 3. Re: Tool to calculate CSP and NOE for DNA trajectory?
> > > > (Kenneth Huang)
> > > > 4. Re: Small molecules paramters (Gustaf Olsson)
> > > > 5. Re: adding hydrogen to pdbqt ligand files (Eduardo Mayo)
> > > > 6. Amber20 Performance on RTX (Turing): known problems, with a
> > > > patch forthcoming (David Cerutti)
> > > > 7. questions for mdgx-virtual site (Gao J)
> > > > 8. Re: questions for mdgx-virtual site (David Cerutti)
> > > > 9. Re: questions for mdgx-virtual site (David Cerutti)
> > > > 10. igb for non-aqueous solvent? (Timothy Schutt)
> > > > 11. Re: cellulose chain (Pinky Mazumder)
> > > > 12. Re: Small molecules paramters (Gustavo Seabra)
> > > > 13. Re: cellulose chain (David A Case)
> > > >
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Thu, 28 May 2020 18:51:16 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] Amber20 pmemd.cuda installation and performance
> > > > problems
> > > > To: Thomas Zeiser <thomas.zeiser.fau.de>, AMBER Mailing List
> > > > <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAEmzWj108UxHJDdvTjuGJRyr=
> > Tj7MOjSFL3a5F+GzJVRZ75ocQ.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > I have access to a machine in Darrin York's group that has a properly
> > > > situated RTX-2080Ti, and I have been able to benchmark the code and
> > see the
> > > > performance hit (also, contrary to what I reported on another thread
> > about
> > > > this, the Pascal GP100 is seeing a 5% DECREASE in performance, not an
> > > > increase with Amber20, so the problem is widespread). After further
> > > > consultation with Scott Legrand and one of our NVIDIA technical
> > > > collaborators, we have narrowed the problem to some things that are now
> > > > happening in the non-bonded kernels in order to protect us against
> > > > deprecations that NVIDIA plans to make in CUDA 11 and future releases.
> > > >
> > > > (Thomas, thank you for your efforts, but I think we have already
> > solved the
> > > > problem, at least to the extent that testing on your platforms could
> > inform
> > > > us. I may yet log in if we devise a fix and want to test it on a broad
> > > > array of RTX hardware, but that is an IF.)
> > > >
> > > > In particular, Scott and I looked over the kernel register spills, and
> > > > Amber20 is overall better in this regard than Amber18, although neither
> > > > code has a performance problem in this respect. Scott has also
> > checked in
> > > > some safer, hardware-specific kernel launch bounds and these will be
> > > > applied in a future patch, but what is there is not causing a
> > performance
> > > > problem nor, that we can tell, creating any other issue. Some users,
> > and
> > > > even NVIDIA technicians themselves, have brought up possible
> > performance
> > > > drag resulting from the cmake installation as opposed to the legacy
> > build,
> > > > but I compiled with the legacy build system and I still see a 15% hit
> > on
> > > > RTX-2080Ti, so any impact of cmake is marginal.
> > > >
> > > > In summary, we have traced the performance hit to two kernels, and
> > > > unfortunately they are the most time-consuming kernels in most MD
> > > > applications. While I am still trying to understand the degree that
> > each
> > > > of the necessary changes contributes to the slowdown, the changes are
> > not
> > > > things we can simply revert, and I do not know whether even a major
> > > > overhaul of the non-bonded kernel could mitigate the new CUDA calls
> > that
> > > > will be required in all code going forward. Furthermore, two years
> > ago I
> > > > attempted a major rewrite of the non-bonded routine. After climbing
> > that
> > > > mountain and reaching over the last rock, I looked down to see that the
> > > > code was going to become much more complex, many niche features would
> > have
> > > > been affected, and that while it might be nice for directions I would
> > like
> > > > to see MD go, the new method was not a performance win across the
> > board.
> > > >
> > > > I wish I came with better news, but it appears that this slowdown in
> > > > Amber20 is about where CUDA is going, not the result of any mistakes we
> > > > have made. We may be able to macro-out some of the calls for
> > compilations
> > > > to recover a few percent on legacy chips like Pascal, and the Volta
> > > > architecture (V100 and Titan-V) seems to be resilient in the face of
> > the
> > > > added synchronization calls. However, it looks like the Turing
> > > > architecture performance is going to suffer for the foreseeable future.
> > > > The hope I can offer is that the Ampere chips on the horizon appear to
> > > > resume an upward trend in the compute capacity of a single card, so in
> > time
> > > > simulations will again start to get faster.
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Thu, May 28, 2020 at 2:26 PM Thomas Zeiser <thomas.zeiser.fau.de>
> > wrote:
> > > >
> > > > > On Wed, May 27, 2020 at 08:35:38PM +0200, Thomas Zeiser wrote:
> > > > > > Hi Dave,
> > > > > >
> > > > > > please send me your SSH public key. I'll come back tomorrow with
> > > > > > further instructions.
> > > > >
> > > > > you have to connect with SSH as w17p0001 to port 22622 of
> > > > > grid.rrze.uni-erlangen.de
> > > > > e.g. ssh -4 -p 22622 w17p0001.grid.rrze.uni-erlangen.de
> > > > >
> > > > > That should give you a shell on "testfront1". There, you can use e.g.
> > > > > srun -w medusa --time=10:0:0 --pty /bin/bash
> > > > > to get an interactive job on the node "medusa" which hosts the GPUs.
> > > > >
> > > > > CUDA, etc. are only installed on "medusa". Both testfront1 and
> > > > > medusa can directly access data from the internet (through NAT).
> > > > >
> > > > > While you have a job running on medua, you can also SSH to medusa.
> > > > > Once the job ends, all procces are kill. Thus, if you want to use
> > > > > "screen", run it on testfront1.
> > > > >
> > > > > $HOME has a quota of 10 GB; $WORK of 333 GB.
> > > > >
> > > > >
> > > > > Best
> > > > >
> > > > > thomas
> > > > >
> > > > > > Best
> > > > > >
> > > > > > thomas
> > > > > >
> > > > > > On Wed, May 27, 2020 at 02:29:58PM -0400, David Cerutti wrote:
> > > > > > > This sounds like a great plan. I am about to test amber18 and
> > amber20
> > > > > on a
> > > > > > > local machine in another lab. If I can get access to the server
> > with a
> > > > > > > range of different Turing GPUs I can start to look at how your
> > problem
> > > > > > > takes place.
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > Dave
> > > > > > >
> > > > > > >
> > > > > > > On Wed, May 27, 2020 at 9:08 AM Thomas Zeiser <
> > thomas.zeiser.fau.de>
> > > > > wrote:
> > > > > > >
> > > > > > > > Hi Dave,
> > > > > > > >
> > > > > > > > On Wed, May 27, 2020 at 07:54:32AM -0400, David Cerutti wrote:
> > > > > > > > > I cannot make a meaningful test on an RTX-2080Ti because the
> > card
> > > > > I have
> > > > > > > > > access to are not sufficiently powered to give the right
> > numbers.
> > > > > I see
> > > > > > > > > about a 20% degradation relative to what Ross was able to
> > get.
> > > > > Ditto for
> > > > > > > > > an RTX-6000, which is nearly as fast as a V100 despite
> > having 20%
> > > > > too
> > > > > > > > > little power feeding it.
> > > > > > > >
> > > > > > > > we could provide you temporary access to our HPC systems to
> > support
> > > > > > > > you in investigating the prossible performance degradation.
> > > > > > > >
> > > > > > > > I'd could either offer one host with four different
> > Turing-based
> > > > > > > > GPUs (Geforce 2070 Super, 2080 Super, Quadro RTX 5000, and
> > 6000) or
> > > > > > > > a node with 4x Geforce 2080Ti.
> > > > > > > >
> > > > > > > > Both systems are running Ubuntu 18.04. Cuda toolkits 9.0 up to
> > 10.2
> > > > > > > > are installedi together with driver 440.64.00.
> > Persistence-Mode is
> > > > > > > > enabled on all GPUs. cmake/3.11.1 would also be available as
> > > > > > > > module.
> > > > > > > >
> > > > > > > >
> > > > > > > > Best
> > > > > > > >
> > > > > > > > thomas
> > > > > > > >
> > > > > > > > > Dave
> > > > > > > > --
> > > > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > > > thomas.zeiser.fau.de
> > > > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > > > >
> > > > > >
> > > > > > --
> > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > thomas.zeiser.fau.de
> > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > >
> > > > > --
> > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > thomas.zeiser.fau.de
> > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 2
> > > > Date: Thu, 28 May 2020 21:33:01 -0400
> > > > From: David A Case <david.case.rutgers.edu>
> > > > Subject: Re: [AMBER] Simulating pyridine in water TIP3P
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > 20200529013301.ljprvlrh2piy3nob.vpn-client-172-16-9-226.rutgers.edu>
> > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > >
> > > > On Thu, May 28, 2020, Debarati DasGupta wrote:
> > > >
> > > > >I faced this error in equilibration step. Should I have a smaller cut
> > value?
> > > > >Cutoff list exceeds largest sphere in unit cell!!
> > > >
> > > > No: you need to have a bigger system. When a side of the periodic box
> > > > gets to be less than about 20 Ang., it gets to be too small for Amber
> > to
> > > > handle, since Amber was designed and optimized for larger periodic
> > > > cells.
> > > >
> > > > You may be able to get away with setting skinnb to 1 (instead of its
> > > > default value of 2). That will allow you to go to slightly smaller
> > > > boxes. But it would be rather dangerous to reduce the cutoff value to
> > > > anything below 8 Ang: we cut off Lennard-Jones interactions at "cut",
> > > > and 8 Ang. is already on the edge of being to small.
> > > >
> > > > By far the simplest fix is to just use more water molecules in your
> > > > original setup.
> > > >
> > > > ....dac
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 3
> > > > Date: Thu, 28 May 2020 23:57:59 -0400
> > > > From: Kenneth Huang <kennethneltharion.gmail.com>
> > > > Subject: Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory?
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > CALeh7kALqvra6YccT-Sp4J7sMPJA37ArLhizviAkuUHjsEdrxw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi Christina,
> > > >
> > > > Thanks a lot for the insight and script! That more or less covers for
> > what
> > > > I wanted to do NOE and CSP wise, and LAMORD should more or less fill
> > in the
> > > > gap that the protein CSP softwares I found weren't able to do.
> > > >
> > > > Best,
> > > >
> > > > Kenneth
> > > >
> > > > On Thu, May 28, 2020 at 8:42 AM Christina Bergonzo <
> > cbergonzo.gmail.com>
> > > > wrote:
> > > >
> > > > > Hi Kenneth,
> > > > >
> > > > > I do not know of any stand alone tools that will calculate NMR
> > observables
> > > > > from a trajectory.
> > > > > I regularly do this without too much hassle using a combination of
> > bash/awk
> > > > > scripting and Cpptraj/shifts.
> > > > > I also back out NOE distances from distance restraints - if you want
> > to
> > > > > predict NOEs using a trajectory, that's a different question (see
> > Henriksen
> > > > > et al. JPCB, dx.doi.org/10.1021/jp400530e), but also distance
> > based.
> > > > >
> > > > > If you look at the Cpptraj distance command, there is an option for
> > > > > evaluating a distance as an NOE.
> > > > > I write a script that takes my atoms of interest from whatever
> > experimental
> > > > > file format I have, and formats them into the distance command:
> > > > >
> > > > > distance d0 :1.H1' :1.H4' type noe bound 0.0 bound 7.0 out
> > > > > dist/noe.val.0.dat
> > > > > ....
> > > > > distance d50 :6.H5'' :6.H6 type noe bound 0.0 bound 7.0 out
> > > > > dist/noe.val.50.dat
> > > > > analyze statistics all out noe.dat
> > > > >
> > > > > The last part dumps analysis of each distance into a file (noe.dat)
> > > > > containing initial and final values, avg and standard deviation,
> > 1/r^6
> > > > > averages, # of violations, etc.
> > > > > Example output:
> > > > >
> > > > > STATISTICS :1.H1' and :1.H4'
> > > > > AVERAGE: 3.0492 (0.2559 stddev)
> > > > > INITIAL: 3.0944
> > > > > FINAL: 3.2662
> > > > > NOE SERIES: S < 2.9, M < 3.5, W < 5.0, blank otherwise.
> > > > > |SMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM|
> > > > > NOE < 7.00 for 100.00% of the time
> > > > > NOE <r^-6>^(-1/6)= 2.9650
> > > > > #Violations: Low= 0 High= 0 Total= 0
> > > > > Rexp= 7.0000 <Violation>= -4.0350
> > > > >
> > > > > < 2.5 2.5-3.5 3.5-4.5 4.5-5.5 5.5-6.5 > 6.5
> > > > > -------------------------------------------------------
> > > > > %occupied | 2.4 | 95.1 | 2.5 | | | |
> > > > > average | 2.402 | 3.051 | 3.611 | | | |
> > > > > stddev | 0.084 | 0.223 | 0.103 | | | |
> > > > > -------------------------------------------------------
> > > > > __________________________________________________________________
> > > > >
> > > > > For chemical shifts for nucleic acids, I use shifts for protons, and
> > > > > there's larmor-D for proton and carbon shifts.
> > > > > And, I go through a similar procedure, where I look at the
> > experiment to
> > > > > see what's be deposited, use shifts to calculate those values from
> > PDBs (I
> > > > > have found you'll need to rename 5' and 3' ends to their non-terminal
> > > > > counterparts i.e., C3 to C), and then calculate for each frame and
> > average.
> > > > >
> > > > > Good luck!
> > > > > -Christina
> > > > >
> > > > > On Wed, May 27, 2020 at 7:48 PM Kenneth Huang <
> > kennethneltharion.gmail.com
> > > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > A general question- does anyone know of tools (assuming there
> > isn't a
> > > > > > combined suite) for calculating CSP or NOEs from a trajectory? I
> > know
> > > > > > there's SPARTA+ and shiftX2 for protein CSPs for proteins, but
> > with DNA
> > > > > all
> > > > > > I've seen is the NMR option in Gaussian, which seems prohibitively
> > > > > > expensive.
> > > > > >
> > > > > > Likewise for NOEs I know of MD2NOE but haven't ever used it in
> > context of
> > > > > > DNA, and other than back-calculating from the distance restraints,
> > I was
> > > > > > just wondering if there had been any other options in cpptraj?
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Kenneth
> > > > > > --
> > > > > > Ask yourselves, all of you, what power would hell have if those
> > > > > imprisoned
> > > > > > here could not dream of heaven?
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > -----------------------------------------------------------------
> > > > > Christina Bergonzo
> > > > > Research Chemist
> > > > > Biomolecular Measurement Division, MML, NIST
> > > > > -----------------------------------------------------------------
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Ask yourselves, all of you, what power would hell have if those
> > imprisoned
> > > > here could not dream of heaven?
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 4
> > > > Date: Fri, 29 May 2020 05:53:03 +0000
> > > > From: Gustaf Olsson <gustaf.olsson.lnu.se>
> > > > Subject: Re: [AMBER] Small molecules paramters
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID: <EDDA8042-177F-409D-9875-76E4A5AA9EF2.lnu.se>
> > > > Content-Type: text/plain; charset="utf-8"
> > > >
> > > > According to the fifth information webpage
> > > >
> > > > ?Amber-compatible parameters can also be generated, although
> > Amber-style force field files are not output (users can convert though with
> > parmed)?
> > > > - http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> > > >
> > > > It should be very possible. If it is advisable, I suspect that depends
> > on the quality of generated parameters.
> > > >
> > > > Best regards
> > > > // Gustaf
> > > >
> > > >
> > > > On 28 May 2020, at 14:47, Athena N <athena.nas01.gmail.com<mailto:
> > athena.nas01.gmail.com>> wrote:
> > > >
> > > > Hi all,
> > > >
> > > > I want to know if it advisable to use any other force fields than gaff
> > for
> > > > small molecules like some indole and pyridine systems.? If we generate
> > some
> > > > parameters using fftk (force field tool kit), could we use those and
> > do the
> > > > simulation in AMBER?
> > > >
> > > > Thank you all
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 5
> > > > Date: Fri, 29 May 2020 02:25:00 -0400
> > > > From: Eduardo Mayo <eduardomayoyanes.gmail.com>
> > > > Subject: Re: [AMBER] adding hydrogen to pdbqt ligand files
> > > > To: amber.ambermd.org
> > > > Message-ID:
> > > > <CAFVrw=SeTENo9zGCZO3vHbQ=
> > ruZGs8HFYVJNv6WYqY2yaMwxyw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi!
> > > > I recommend:
> > > > 1 convert to .mol file using babel (with and without -h) and check if
> > the
> > > > tautomeric state is the desired.
> > > > 2 if 1 didn't work then covert to smarts or smiles( so if you got a
> > > > tautomeric state with local charge the smarts/smiles will have this
> > > > information) . Use rdkit to covert smiles/smarts to rdkit.Mol and add
> > then
> > > > the hydrogen. Chem.Embedded the molecule so you have a 3D model. The
> > read
> > > > the mol file using Chem.MolFromMolFile. Align (you may need find the
> > mcse)
> > > > the molecule obtained from smiles to the molecule obtained from the mol
> > > > file.
> > > >
> > > >
> > > >
> > > >
> > > > Message: 3
> > > > Date: Tue, 28 Apr 2020 21:15:36 +0000 (UTC)
> > > > From: Marawan Hussien <marawanhussain.yahoo.com>
> > > > Subject: [AMBER] adding hydrogen to pdbqt ligand files
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID: <1174479232.1819345.1588108536730.mail.yahoo.com>
> > > > Content-Type: text/plain; charset=UTF-8
> > > >
> > > > Is there is a standard leap command to add hydrogen atoms to non-polar
> > > > atoms (carbons) only during system building? I am preparing a
> > > > protein-ligand system for MD from pdbqt protein-ligand complex and do
> > not
> > > > want to change the ligand tautomeric state.? I tried rdkit, obabel,
> > chimera
> > > > but every tool I tried will add hydrogen to the entire molecule, not
> > carbon
> > > > atoms only? Any suggestion?
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 6
> > > > Date: Fri, 29 May 2020 02:30:20 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: [AMBER] Amber20 Performance on RTX (Turing): known problems,
> > > > with a patch forthcoming
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > CAEmzWj2pfjPxJg0-O+th+VyMcBsjFhqERfM0AJDtxZAzps6v2Q.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Dear Users,
> > > >
> > > > As has been shared on this listserv, many users are finding that
> > Amber20 is
> > > > not as fast on Turing architectures for PME simulations as Amber18.
> > The
> > > > source of this problem has now been identified, and indeed it affects
> > much
> > > > more than just Turing, but the 15-20% slowdown seen on Turing is
> > merely the
> > > > most severe case.
> > > >
> > > > The slowdown itself does NOT reflect any bugs or issues that would
> > > > necessitate repeating experiments. The problem, rather, is that some
> > > > future-proofing that our collaborators at NVIDIA kindly performed for
> > us
> > > > has led to more GPU effort in synchronization. The benefit of this is
> > > > that, come CUDA 11 and the new Ampere chipset, pmemd.cuda is already
> > > > prepared to run on the cards (at a substantially greater speed than is
> > > > currently possible with a V100, which in my view competes with
> > RTX-6000 for
> > > > top dog). However, legacy chipsets that do not need to perform the
> > > > synchronization required for CUDA 11 to work properly will suffer in
> > > > performance.
> > > >
> > > > Contrary to what I warned yesterday afternoon, a fix is possible and we
> > > > already have it. A compiler-specific directive will create separate
> > code
> > > > paths for the various chipsets and mask out the synchronization where
> > it is
> > > > not needed, recovering the Amber18 performance while still keeping the
> > code
> > > > in a state that is ready for the next architecture.
> > > >
> > > > I would like to thank Scott Legrand, Peng Wang, and others at NVIDIA
> > who
> > > > contributed either to the future-proofing or the short-term recovery
> > > > effort. As you sit at home preparing your new simulations, please
> > enjoy
> > > > some ice cream or other simple treat while you await the forthcoming
> > patch
> > > > that will put Amber20 back where it should be on the benchmarks.
> > > >
> > > > Sincerely,
> > > >
> > > > Dave Cerutti
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 7
> > > > Date: Fri, 29 May 2020 16:29:44 +0800 (GMT+08:00)
> > > > From: "Gao J" <21919039.zju.edu.cn>
> > > > Subject: [AMBER] questions for mdgx-virtual site
> > > > To: amber.ambermd.org
> > > > Message-ID: <59110ff3.e289d.1725f8d21aa.Coremail.21919039.zju.edu.cn>
> > > > Content-Type: text/plain; charset=UTF-8
> > > >
> > > > Hello
> > > >
> > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > repulsions between themselves merely. My parameters for &rule were as
> > follows and I got an error said "ReadEPRuleFile >> Error. Extra point name
> > unspecified." So I wonder what the correct format of "epname" or "atom"
> > required. What's more, I am a little confused if any parameters needed for
> > "excl[1,2]".
> > > >
> > > > I really appreciate for your help!
> > > >
> > > > &rule
> > > >
> > > > frame[1,2]: C1 C4
> > > >
> > > > epname: VSB
> > > >
> > > > atom: VSB
> > > >
> > > > style: 1
> > > >
> > > > excl[1,2]
> > > >
> > > > v12: 0.5
> > > >
> > > > Sig: 21
> > > >
> > > > eps: 0.01
> > > >
> > > > residue: UNK
> > > >
> > > > &end
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 8
> > > > Date: Fri, 29 May 2020 05:42:42 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > CAEmzWj1n-DX_UodrWv9srcjbPRDDb03vmabfuFwTo5Rau6SO3w.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > OK, so good evening! mdgx is not going to be FAST simulator but if you
> > > > just need to get a system running a few thousand (or even million)
> > steps of
> > > > MD then it'll do fine. I am working right now to enable this virtual
> > site
> > > > functionality in pmemd and also tleap, so with luck it'll be possible
> > to
> > > > create more interesting molecular models in the standard MD engines
> > soon.
> > > >
> > > > For the &rule namelist, it's... a &namelist, just like &cntrl or
> > &ewald in
> > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > technically the Fortran standard, but it gets things pretty well and
> > lets
> > > > you have some flexibility. I would try writing this first:
> > > >
> > > > &rule
> > > > frame1 = "C1",
> > > > frame2 = "C2",
> > > > epname = "VSB",
> > > > style = 1,
> > > > v12 = 0.5,
> > > > sig = 2.1,
> > > > eps = 0.05,
> > > > residue = "UNK",
> > > > &end
> > > >
> > > > In your input, you have lots of colon punctuation (:) that mdgx won't
> > know
> > > > how to parse (nor will sander or pmemd). And I've written the above in
> > > > shorthand. There are aliases for all those keywords if you find one
> > or the
> > > > other easier to remember ("sig" can also be "Sigma"), but the keywords
> > ARE
> > > > case-sensitive. The "epname" keyword actually has four aliases,
> > "epname",
> > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard
> > there.)
> > > >
> > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > points: if they're right on the middle of a bond, or equally close to
> > more
> > > > than one real atom in general, how do we count their exclusions? (This
> > is a
> > > > reason that one of the experienced force field developers I work with
> > > > demands that all of these extra points be close to their ONE parent
> > atom
> > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > definition, an extra point is 1:1 to its parent atom, so all non-bonded
> > > > exclusions of the frame1 atom will be inherited by the extra point.
> > But if
> > > > you specify excl2, it's going to take your frame2 atom and say that the
> > > > extra point is also 1:1 to that. Ditto for excl3, so the extra point
> > is
> > > > accumulating more and more exclusions, atoms that it will not count
> > > > interactions with.
> > > >
> > > > This makes me realize that I need to document this part of the code a
> > bit
> > > > better, specifically in the onboard manual. There are descriptions
> > for all
> > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command
> > line.
> > > > But not for &rule...
> > > >
> > > > Happy to help more, and you are not the first to make use of mdgx to
> > create
> > > > some very unorthodox (not unusual, just not what the typical programs
> > > > simulate) molecular models. It HAS been done before, and not just by
> > me :-)
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > >
> > > > > Hello
> > > > >
> > > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > > repulsions between themselves merely. My parameters for &rule were as
> > > > > follows and I got an error said "ReadEPRuleFile >> Error. Extra
> > point name
> > > > > unspecified." So I wonder what the correct format of "epname" or
> > "atom"
> > > > > required. What's more, I am a little confused if any parameters
> > needed for
> > > > > "excl[1,2]".
> > > > >
> > > > > I really appreciate for your help!
> > > > >
> > > > > &rule
> > > > >
> > > > > frame[1,2]: C1 C4
> > > > >
> > > > > epname: VSB
> > > > >
> > > > > atom: VSB
> > > > >
> > > > > style: 1
> > > > >
> > > > > excl[1,2]
> > > > >
> > > > > v12: 0.5
> > > > >
> > > > > Sig: 21
> > > > >
> > > > > eps: 0.01
> > > > >
> > > > > residue: UNK
> > > > >
> > > > > &end
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 9
> > > > Date: Fri, 29 May 2020 05:49:46 -0400
> > > > From: David Cerutti <dscerutti.gmail.com>
> > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAEmzWj3n5=
> > jWdmadVwoi-DVsCWC90bGnhNQ7440eWsoDWEPLnQ.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Another note: if you are trying to simulate a mixture of two solvents
> > and
> > > > finding that the two molecular models do not want to stay mixed, this
> > is a
> > > > well-known problem in many models. If you want to just have virtual
> > sites
> > > > (extra points) sticking out of the benzene to push benzenes away from
> > each
> > > > other, that's one way to do it but it sounds extremely "staged" shall
> > we
> > > > say. It would be like you've contrived the model and getting any
> > useful
> > > > properties out of it would be a hard sell. I'm not actually sure you
> > could
> > > > do this--mdgx is going to see the LJ parameters you assign to the
> > virtual
> > > > sites and then try to apply the reigning LJ combining rule to
> > determine how
> > > > they interact with other atoms. So they'd interact with ALL other
> > atoms of
> > > > the simulation according to Lorentz-Berthelot combining rules, I
> > expect,
> > > > not just other virtual sites.
> > > >
> > > > Dave
> > > >
> > > >
> > > > On Fri, May 29, 2020 at 5:42 AM David Cerutti <dscerutti.gmail.com>
> > wrote:
> > > >
> > > > > OK, so good evening! mdgx is not going to be FAST simulator but if
> > you
> > > > > just need to get a system running a few thousand (or even million)
> > steps of
> > > > > MD then it'll do fine. I am working right now to enable this
> > virtual site
> > > > > functionality in pmemd and also tleap, so with luck it'll be
> > possible to
> > > > > create more interesting molecular models in the standard MD engines
> > soon.
> > > > >
> > > > > For the &rule namelist, it's... a &namelist, just like &cntrl or
> > &ewald in
> > > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > > technically the Fortran standard, but it gets things pretty well and
> > lets
> > > > > you have some flexibility. I would try writing this first:
> > > > >
> > > > > &rule
> > > > > frame1 = "C1",
> > > > > frame2 = "C2",
> > > > > epname = "VSB",
> > > > > style = 1,
> > > > > v12 = 0.5,
> > > > > sig = 2.1,
> > > > > eps = 0.05,
> > > > > residue = "UNK",
> > > > > &end
> > > > >
> > > > > In your input, you have lots of colon punctuation (:) that mdgx
> > won't know
> > > > > how to parse (nor will sander or pmemd). And I've written the above
> > in
> > > > > shorthand. There are aliases for all those keywords if you find one
> > or the
> > > > > other easier to remember ("sig" can also be "Sigma"), but the
> > keywords ARE
> > > > > case-sensitive. The "epname" keyword actually has four aliases,
> > "epname",
> > > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard
> > there.)
> > > > >
> > > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > > points: if they're right on the middle of a bond, or equally close
> > to more
> > > > > than one real atom in general, how do we count their exclusions?
> > (This is a
> > > > > reason that one of the experienced force field developers I work with
> > > > > demands that all of these extra points be close to their ONE parent
> > atom
> > > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > > definition, an extra point is 1:1 to its parent atom, so all
> > non-bonded
> > > > > exclusions of the frame1 atom will be inherited by the extra point.
> > But if
> > > > > you specify excl2, it's going to take your frame2 atom and say that
> > the
> > > > > extra point is also 1:1 to that. Ditto for excl3, so the extra
> > point is
> > > > > accumulating more and more exclusions, atoms that it will not count
> > > > > interactions with.
> > > > >
> > > > > This makes me realize that I need to document this part of the code
> > a bit
> > > > > better, specifically in the onboard manual. There are descriptions
> > for all
> > > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command
> > line.
> > > > > But not for &rule...
> > > > >
> > > > > Happy to help more, and you are not the first to make use of mdgx to
> > > > > create some very unorthodox (not unusual, just not what the typical
> > > > > programs simulate) molecular models. It HAS been done before, and
> > not just
> > > > > by me :-)
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > > >
> > > > >> Hello
> > > > >>
> > > > >> I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > >> ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > >> repulsions between themselves merely. My parameters for &rule were
> > as
> > > > >> follows and I got an error said "ReadEPRuleFile >> Error. Extra
> > point name
> > > > >> unspecified." So I wonder what the correct format of "epname" or
> > "atom"
> > > > >> required. What's more, I am a little confused if any parameters
> > needed for
> > > > >> "excl[1,2]".
> > > > >>
> > > > >> I really appreciate for your help!
> > > > >>
> > > > >> &rule
> > > > >>
> > > > >> frame[1,2]: C1 C4
> > > > >>
> > > > >> epname: VSB
> > > > >>
> > > > >> atom: VSB
> > > > >>
> > > > >> style: 1
> > > > >>
> > > > >> excl[1,2]
> > > > >>
> > > > >> v12: 0.5
> > > > >>
> > > > >> Sig: 21
> > > > >>
> > > > >> eps: 0.01
> > > > >>
> > > > >> residue: UNK
> > > > >>
> > > > >> &end
> > > > >>
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> AMBER.ambermd.org
> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 10
> > > > Date: Fri, 29 May 2020 08:40:59 -0500
> > > > From: Timothy Schutt <tschutt7.gmail.com>
> > > > Subject: [AMBER] igb for non-aqueous solvent?
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAGGi8+gfyC=aCWfrDO+8oEpWCOzyTBnGQqUja4yv=
> > 9w1o2Bm5A.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Hi Amber Folks!
> > > >
> > > > Is it an okay approximation to use igb=1 and extdiel=*dielectric
> > value* to
> > > > represent a non-aqueous solvent implicitly?
> > > >
> > > > I would like to investigate some surface binding interactions of a
> > > > non-aqueous solvent but the solvents are too viscous to get decent
> > sampling
> > > > in a reasonable time frame so my thought was to use 2D umbrella
> > sampling
> > > > across the surface sites using just one explicit solvent molecule with
> > the
> > > > rest being implicit. In each solvent system I would use the different
> > one
> > > > explicit solvent and the approrpiate external dielectric for that
> > solvent
> > > > in bulk. Would that be an accurate enough approach to provide reliable
> > > > trends of mapping different solvents interactions with the surface?
> > > >
> > > > Any advice is greatly appreciated, Thanks!
> > > >
> > > > -Tim
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 11
> > > > Date: Fri, 29 May 2020 09:46:58 -0500
> > > > From: Pinky Mazumder <pmazumder67.gmail.com>
> > > > Subject: Re: [AMBER] cellulose chain
> > > > To: AMBER Mailing List <amber.ambermd.org>, Lachele Foley
> > > > <lf.list.gmail.com>
> > > > Message-ID:
> > > > <
> > CAFoDHbjw9EqX4ewswc+agnru_2pRMZR2kssyXzUjW0u5x7GRQw.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Thank you.
> > > >
> > > > I can place the chains parallel to each other. After that, I need to
> > see
> > > > the h-bond interaction between the polymers. For that I ran the
> > simulations
> > > > with energy minimization, heating and production MD.
> > > >
> > > > Even after, I do not see the H-Bond. To do so, what process I need to
> > > > follow?
> > > >
> > > > Thank you.
> > > >
> > > > Sincerely,
> > > > Pinky
> > > >
> > > > On Sat, May 16, 2020 at 4:33 AM Lachele Foley <lf.list.gmail.com>
> > wrote:
> > > >
> > > > > When you copy the chains, they have exactly the same x,y,z
> > > > > coordinates. In other words, they are right on top of each other.
> > > > >
> > > > > You will need to use the translate and/or transpose commands to put
> > > > > them into the proper relative geometries.
> > > > >
> > > > > On Fri, May 15, 2020 at 11:53 PM Pinky Mazumder <
> > pmazumder67.gmail.com>
> > > > > wrote:
> > > > > >
> > > > > > Please discard my previous message.
> > > > > >
> > > > > >
> > > > > > Thank you so much for your cordial response.
> > > > > >
> > > > > >
> > > > > > I can copy the chain using this command and the numbers of atoms
> > are
> > > > > > increasing.
> > > > > >
> > > > > >
> > > > > > However, I am not able to see the two chains together in vmd or in
> > the
> > > > > > xleap using the edit command.
> > > > > >
> > > > > >
> > > > > > Could you please help me in this regard?
> > > > > >
> > > > > >
> > > > > > Thank you again.
> > > > > >
> > > > > > Sincerely,
> > > > > > Pinky
> > > > > >
> > > > > > On Fri, May 15, 2020 at 10:51 PM Pinky Mazumder <
> > pmazumder67.gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Thank you so much for your cordial response.
> > > > > > >
> > > > > > >
> > > > > > > But, I can show the two chains together using vmd. I can copying
> > the
> > > > > chain
> > > > > > > because the numbers of atoms are increasing.
> > > > > > >
> > > > > > >
> > > > > > > However, I am not able to see the two chains together.
> > > > > > >
> > > > > > >
> > > > > > > Could you please help me in this regard?
> > > > > > >
> > > > > > >
> > > > > > > Thank you again.
> > > > > > >
> > > > > > > Sincerely,
> > > > > > >
> > > > > > > On Fri, May 15, 2020 at 10:09 PM Lachele Foley <
> > lf.list.gmail.com>
> > > > > wrote:
> > > > > > >
> > > > > > >> First, you need to know the geometric relationships between the
> > > > > > >> chains. The relationships will differ based on the source of
> > the
> > > > > > >> cellulose.
> > > > > > >>
> > > > > > >> In leap, you can use:
> > > > > > >>
> > > > > > >> chain2 = copy chain1
> > > > > > >>
> > > > > > >> to make a copy of a chain.
> > > > > > >>
> > > > > > >> Then, once you know the relative geometries, you can use
> > translate
> > > > > > >> and/or transform to position the chains properly with respect
> > to each
> > > > > > >> other.
> > > > > > >>
> > > > > > >> Alternatively, find an experimentally-determined structure,
> > such as an
> > > > > > >> X-ray or cryo-EM structure.
> > > > > > >>
> > > > > > >> Also consider contacting Dr. Jodi Hadden. She can probably
> > help you,
> > > > > > >> but she's pretty busy with other stuff, so you might have to be
> > > > > > >> patient.
> > > > > > >>
> > > > > > >> On Fri, May 15, 2020 at 1:01 PM Pinky Mazumder <
> > pmazumder67.gmail.com
> > > > > >
> > > > > > >> wrote:
> > > > > > >> >
> > > > > > >> > Hi David,
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Thank you for your response.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > I have been able to make the polymer of cellulose. But I need
> > > > > multiple
> > > > > > >> > chains together.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Could you please suggest how can I replicate the same polymer
> > chain
> > > > > or
> > > > > > >> can
> > > > > > >> > I build the multiple number of polymer chain together?
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Is there any specific tutorial or command that I need to
> > follow?
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Thank you.
> > > > > > >> >
> > > > > > >> >
> > > > > > >> > Kind regards,
> > > > > > >> >
> > > > > > >> > Pinky
> > > > > > >> >
> > > > > > >> > On Sun, Apr 5, 2020, 12:20 PM David A Case <
> > david.case.rutgers.edu>
> > > > > > >> wrote:
> > > > > > >> >
> > > > > > >> > > On Thu, Apr 02, 2020, Pinky Mazumder wrote:
> > > > > > >> > > >
> > > > > > >> > > >I want to build a chain of cellulose. So when I am trying
> > to do
> > > > > this
> > > > > > >> by
> > > > > > >> > > >using foo sequence command.
> > > > > > >> > > >
> > > > > > >> > > > It says that '' Error : sequence : ILLEGAL UNIT named
> > Glc''.
> > > > > > >> > >
> > > > > > >> > > Are you inside tleap at this point? If so, execute the
> > "list"
> > > > > > >> command,
> > > > > > >> > > and see if Glc is one of the units listed. If not, you
> > would
> > > > > need to
> > > > > > >> > > somehow load the units you want.
> > > > > > >> > >
> > > > > > >> > > Carbohydrates are discussed in Chap. 3 of the Amber
> > Reference
> > > > > Manual:
> > > > > > >> > > you might see if that would help.
> > > > > > >> > >
> > > > > > >> > > If this is not a tleap error, then please give more details
> > about
> > > > > > >> > > exactly what you mean by "using foo sequence command".
> > > > > > >> > >
> > > > > > >> > > ...thx...dac
> > > > > > >> > >
> > > > > > >> > >
> > > > > > >> > > _______________________________________________
> > > > > > >> > > AMBER mailing list
> > > > > > >> > > AMBER.ambermd.org
> > > > > > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >> > >
> > > > > > >> > _______________________________________________
> > > > > > >> > AMBER mailing list
> > > > > > >> > AMBER.ambermd.org
> > > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >> --
> > > > > > >> :-) Lachele
> > > > > > >> Lachele Foley
> > > > > > >> CCRC/UGA
> > > > > > >> Athens, GA USA
> > > > > > >>
> > > > > > >> _______________________________________________
> > > > > > >> AMBER mailing list
> > > > > > >> AMBER.ambermd.org
> > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Pinky, Sharmi
> > > > > > > AL,US
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Pinky, Sharmi
> > > > > > AL,US
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > :-) Lachele
> > > > > Lachele Foley
> > > > > CCRC/UGA
> > > > > Athens, GA USA
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > --
> > > > Pinky, Sharmi
> > > > AL,US
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 12
> > > > Date: Fri, 29 May 2020 12:20:56 -0400
> > > > From: Gustavo Seabra <gustavo.seabra.gmail.com>
> > > > Subject: Re: [AMBER] Small molecules paramters
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <CAO4guEKk=
> > 2u1gnzrdBp8hSCDsV5yaN2Q52Muip+SW3_QcOW_hg.mail.gmail.com>
> > > > Content-Type: text/plain; charset="UTF-8"
> > > >
> > > > Although it is possible to convert parameters to AMBER *format*, so
> > they
> > > > can be read by AMBER, this is not the ideal. Bear in mind that the MD
> > force
> > > > fields rely on a fine balance between charges and force constants
> > > > obtained from multiple calculations, and that each force field "flavor"
> > > > uses a different methodology to obtain those parameters. So, ideally,
> > you
> > > > will want to use for your small molecule the same methodology that was
> > used
> > > > to derive parameters for the rest of the system, or at least have some
> > > > indication that the parameters are compatible. GAFF (ad GAFF2) have
> > been
> > > > developed with that in mind, so their parameters are, in principle,
> > > > compatible with the Amber force fields. If you get the parameters from
> > > > other sources, make sure you do some extra testing.
> > > >
> > > > All the best,
> > > > --
> > > > Gustavo Seabra.
> > > >
> > > >
> > > > On Thu, May 28, 2020 at 8:47 AM Athena N <athena.nas01.gmail.com>
> > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I want to know if it advisable to use any other force fields than
> > gaff for
> > > > > small molecules like some indole and pyridine systems.? If we
> > generate some
> > > > > parameters using fftk (force field tool kit), could we use those and
> > do the
> > > > > simulation in AMBER?
> > > > >
> > > > > Thank you all
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > Message: 13
> > > > Date: Fri, 29 May 2020 12:32:06 -0400
> > > > From: David A Case <david.case.rutgers.edu>
> > > > Subject: Re: [AMBER] cellulose chain
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Message-ID:
> > > > <
> > 20200529163206.k2wr3wlvv2kcwtee.vpn-client-172-16-9-226.rutgers.edu>
> > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > >
> > > > On Fri, May 29, 2020, Pinky Mazumder wrote:
> > > > >
> > > > >I can place the chains parallel to each other. After that, I need to
> > see
> > > > >the h-bond interaction between the polymers. For that I ran the
> > simulations
> > > > >with energy minimization, heating and production MD.
> > > > >
> > > > >Even after, I do not see the H-Bond. To do so, what process I need to
> > > > >follow?
> > > >
> > > > I guessing you need a better starting structure. Do the chains move
> > > > much during the simulation? If there are no inter-chain hydrogen bonds
> > > > in the starting structure, it may difficult to get them to form just
> > > > with MD, even if the H-bonded structure has a lower free energy.
> > > >
> > > > You may be able to get some good ideas, plus a feeling for how mobile
> > > > your chains are, by looking at the trajectories you have. Generally,
> > MD
> > > > simluations sample configurations close to the starting point, and
> > > > either long simulations or advanced sampling methods are required to
> > > > find quite different structures.
> > > >
> > > > If you know what H-bonds you would like to form, you could add
> > > > restraints (called "NMR" restraints in Amber lingo, for historical
> > > > reasons) that will pull the H-bond donor and acceptor atoms to an
> > > > H-bonding geometry.
> > > >
> > > > ....good luck...dac
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > > End of AMBER Digest, Vol 3017, Issue 1
> > > > **************************************
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Sat, 30 May 2020 22:18:49 -0400
> > > From: "Baker, Joseph" <bakerj.tcnj.edu>
> > > Subject: [AMBER] amber20 output header
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAA5VDpDRkhf2OffxXdNd1dXZxA=
> > Nu9wv580Go8+JUMuKDLEE4Q.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Hi all,
> > >
> > > In my output log files when running pmemd.cuda in Amber20 I get the
> > > following (Amber 20 PMEMD but then a comment about release 18). pmemd
> > > --version says Version 20 in this case.
> > >
> > > ------------------------------------------------------- Amber 20 PMEMD
> > 2020
> > > -------------------------------------------------------| PMEMD
> > > implementation of SANDER, Release 18
> > >
> > > But this made me curious, and I've noticed too that when looking at some
> > of
> > > my Amber18 output logs in the output it reports Amber 18 and Release 18,
> > > but doing pmemd --version with Amber18 loaded reports Version 16.
> > >
> > > Are these just misprints in the output header info (for version 20) and
> > in
> > > the version info for Amber18?
> > >
> > > Thanks!
> > > Joe
> > >
> > > ------
> > > Joseph Baker, PhD
> > > Associate Professor
> > > Department of Chemistry
> > > C212 Science Complex
> > > The College of New Jersey
> > > Ewing, NJ 08628
> > > Phone: (609) 771-3173
> > > Web: http://bakerj.pages.tcnj.edu/
> > > Pronouns: he/him/his
> > >
> > > Chair (2020), Trenton Local Section of the ACS
> > > Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> > > Research
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Sat, 30 May 2020 23:56:46 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: Re: [AMBER] amber20 output header
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <CAEmzWj1KSEHGjSi5_F319cTcN=_
> > tuimWH0+7WcjK8eSHU3_VOw.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > I'm currently without network access to the code, but this looks like a
> > > misprint in both cases. Someone, like me, could do a 'grep " 18 "
> > src/*/*'
> > > command to see all instances of that 18. But please be assured, you've
> > got
> > > Amber20.
> > >
> > > Dave
> > >
> > >
> > > On Sat, May 30, 2020 at 10:19 PM Baker, Joseph <bakerj.tcnj.edu> wrote:
> > >
> > > > Hi all,
> > > >
> > > > In my output log files when running pmemd.cuda in Amber20 I get the
> > > > following (Amber 20 PMEMD but then a comment about release 18). pmemd
> > > > --version says Version 20 in this case.
> > > >
> > > > ------------------------------------------------------- Amber 20 PMEMD
> > 2020
> > > > -------------------------------------------------------| PMEMD
> > > > implementation of SANDER, Release 18
> > > >
> > > > But this made me curious, and I've noticed too that when looking at
> > some of
> > > > my Amber18 output logs in the output it reports Amber 18 and Release
> > 18,
> > > > but doing pmemd --version with Amber18 loaded reports Version 16.
> > > >
> > > > Are these just misprints in the output header info (for version 20)
> > and in
> > > > the version info for Amber18?
> > > >
> > > > Thanks!
> > > > Joe
> > > >
> > > > ------
> > > > Joseph Baker, PhD
> > > > Associate Professor
> > > > Department of Chemistry
> > > > C212 Science Complex
> > > > The College of New Jersey
> > > > Ewing, NJ 08628
> > > > Phone: (609) 771-3173
> > > > Web: http://bakerj.pages.tcnj.edu/
> > > > Pronouns: he/him/his
> > > >
> > > > Chair (2020), Trenton Local Section of the ACS
> > > > Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> > > > Research
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Sat, 30 May 2020 23:59:36 -0400
> > > From: David Cerutti <dscerutti.gmail.com>
> > > Subject: Re: [AMBER] AMBER Digest, Vol 3017, Issue 1
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Message-ID:
> > > <
> > CAEmzWj3WAjLMW5FpPvdAxHu8wPHSZoTWOhs6k2wbuXja-1xsqQ.mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Please just understand that you're using a pretty old feature here: mdgx,
> > > despite the name, is a force field oriented program. The MD capability
> > is
> > > merely subservient to model building and parameter fitting. I would try
> > to
> > > run with serial (uniprocessor) mdgx until you know that everything works.
> > > If you call excl1 and excl2, the virtual sites (also known as extra
> > points)
> > > will inherit all of the bonded exclusions of those frame atoms. But they
> > > will make non-bonded interactions will all OTHER atoms in the system,
> > > including other virtual sites and other atoms with mass, on other
> > molecules.
> > >
> > > Dave
> > >
> > >
> > > On Sat, May 30, 2020 at 10:19 PM Gao J <21919039.zju.edu.cn> wrote:
> > >
> > > > Hi Dave:
> > > > It's so kind of you to help me.
> > > > I modified my &rule file for a tentative short heating simulation of a
> > > > minimized system, while "mdgx.MPI" neither returned any output nor
> > exited
> > > > with an error for a long time. The only message which seems nonlethal
> > was
> > > > that "Netcdf restart min3.rst does not ave velocity info, Warning:No
> > > > velocities in restart, setting all to 0.0". I had set "irest=0" but no
> > > > randam velocities assigned. Could you please have a check for what's
> > going
> > > > wrong?
> > > > As for your note about the interactions between virtual sites and real
> > > > atoms, what if I exclude both frame1 and frame2 to keep the virtual
> > sites
> > > > out of any nonbonded interaction with real atoms? I am a newcomer of
> > Amber
> > > > and not sure if the combining rule would take these sites into
> > > > consideration in this circumstance.
> > > > Thanks a lot for your gudiance!
> > > > Best
> > > > Gao J
> > > >
> > > > my input file:
> > > > &files
> > > > -p compw.prmtop
> > > > -c min3.rst
> > > > -xpt rule.in
> > > > -o eq1.out
> > > > -r eq1.rst
> > > > -x eq1.mdcrd
> > > > &end
> > > > &cntrl
> > > > imin=0,
> > > >
> > irest=0,nstlim=1000,dt=0.002,cut=8.0,ntb=1,ntpr=500,ntwx=500,ntt=3,gamma_ln=2.0,
> > > > tempi=0.0,temp0=300.0,ioutfm=1,
> > > > &end
> > > > my &rule file:
> > > > &rule
> > > > frame1="C1", frame2="C4", epname="VSB", style=1, excl1, v12=0.5,
> > sig=2.1,
> > > > eps=0.05, residue="UNK",
> > > > &end
> > > >
> > > > > -----????-----
> > > > > ???: amber-request.ambermd.org
> > > > > ????: 2020-05-30 03:00:01 (???)
> > > > > ???: amber.ambermd.org
> > > > > ??:
> > > > > ??: AMBER Digest, Vol 3017, Issue 1
> > > > >
> > > > > Send AMBER mailing list submissions to
> > > > > amber.ambermd.org
> > > > >
> > > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > or, via email, send a message with subject or body 'help' to
> > > > > amber-request.ambermd.org
> > > > >
> > > > > You can reach the person managing the list at
> > > > > amber-owner.ambermd.org
> > > > >
> > > > > When replying, please edit your Subject line so it is more specific
> > > > > than "Re: Contents of AMBER digest..."
> > > > >
> > > > >
> > > > > AMBER Mailing List Digest
> > > > >
> > > > > Today's Topics:
> > > > >
> > > > > 1. Re: Amber20 pmemd.cuda installation and performance problems
> > > > > (David Cerutti)
> > > > > 2. Re: Simulating pyridine in water TIP3P (David A Case)
> > > > > 3. Re: Tool to calculate CSP and NOE for DNA trajectory?
> > > > > (Kenneth Huang)
> > > > > 4. Re: Small molecules paramters (Gustaf Olsson)
> > > > > 5. Re: adding hydrogen to pdbqt ligand files (Eduardo Mayo)
> > > > > 6. Amber20 Performance on RTX (Turing): known problems, with a
> > > > > patch forthcoming (David Cerutti)
> > > > > 7. questions for mdgx-virtual site (Gao J)
> > > > > 8. Re: questions for mdgx-virtual site (David Cerutti)
> > > > > 9. Re: questions for mdgx-virtual site (David Cerutti)
> > > > > 10. igb for non-aqueous solvent? (Timothy Schutt)
> > > > > 11. Re: cellulose chain (Pinky Mazumder)
> > > > > 12. Re: Small molecules paramters (Gustavo Seabra)
> > > > > 13. Re: cellulose chain (David A Case)
> > > > >
> > > > >
> > > > >
> > ----------------------------------------------------------------------
> > > > >
> > > > > Message: 1
> > > > > Date: Thu, 28 May 2020 18:51:16 -0400
> > > > > From: David Cerutti <dscerutti.gmail.com>
> > > > > Subject: Re: [AMBER] Amber20 pmemd.cuda installation and performance
> > > > > problems
> > > > > To: Thomas Zeiser <thomas.zeiser.fau.de>, AMBER Mailing List
> > > > > <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <CAEmzWj108UxHJDdvTjuGJRyr=
> > > > Tj7MOjSFL3a5F+GzJVRZ75ocQ.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > I have access to a machine in Darrin York's group that has a properly
> > > > > situated RTX-2080Ti, and I have been able to benchmark the code and
> > see
> > > > the
> > > > > performance hit (also, contrary to what I reported on another thread
> > > > about
> > > > > this, the Pascal GP100 is seeing a 5% DECREASE in performance, not an
> > > > > increase with Amber20, so the problem is widespread). After further
> > > > > consultation with Scott Legrand and one of our NVIDIA technical
> > > > > collaborators, we have narrowed the problem to some things that are
> > now
> > > > > happening in the non-bonded kernels in order to protect us against
> > > > > deprecations that NVIDIA plans to make in CUDA 11 and future
> > releases.
> > > > >
> > > > > (Thomas, thank you for your efforts, but I think we have already
> > solved
> > > > the
> > > > > problem, at least to the extent that testing on your platforms could
> > > > inform
> > > > > us. I may yet log in if we devise a fix and want to test it on a
> > broad
> > > > > array of RTX hardware, but that is an IF.)
> > > > >
> > > > > In particular, Scott and I looked over the kernel register spills,
> > and
> > > > > Amber20 is overall better in this regard than Amber18, although
> > neither
> > > > > code has a performance problem in this respect. Scott has also
> > checked
> > > > in
> > > > > some safer, hardware-specific kernel launch bounds and these will be
> > > > > applied in a future patch, but what is there is not causing a
> > performance
> > > > > problem nor, that we can tell, creating any other issue. Some
> > users, and
> > > > > even NVIDIA technicians themselves, have brought up possible
> > performance
> > > > > drag resulting from the cmake installation as opposed to the legacy
> > > > build,
> > > > > but I compiled with the legacy build system and I still see a 15%
> > hit on
> > > > > RTX-2080Ti, so any impact of cmake is marginal.
> > > > >
> > > > > In summary, we have traced the performance hit to two kernels, and
> > > > > unfortunately they are the most time-consuming kernels in most MD
> > > > > applications. While I am still trying to understand the degree that
> > each
> > > > > of the necessary changes contributes to the slowdown, the changes
> > are not
> > > > > things we can simply revert, and I do not know whether even a major
> > > > > overhaul of the non-bonded kernel could mitigate the new CUDA calls
> > that
> > > > > will be required in all code going forward. Furthermore, two years
> > ago I
> > > > > attempted a major rewrite of the non-bonded routine. After climbing
> > that
> > > > > mountain and reaching over the last rock, I looked down to see that
> > the
> > > > > code was going to become much more complex, many niche features would
> > > > have
> > > > > been affected, and that while it might be nice for directions I would
> > > > like
> > > > > to see MD go, the new method was not a performance win across the
> > board.
> > > > >
> > > > > I wish I came with better news, but it appears that this slowdown in
> > > > > Amber20 is about where CUDA is going, not the result of any mistakes
> > we
> > > > > have made. We may be able to macro-out some of the calls for
> > > > compilations
> > > > > to recover a few percent on legacy chips like Pascal, and the Volta
> > > > > architecture (V100 and Titan-V) seems to be resilient in the face of
> > the
> > > > > added synchronization calls. However, it looks like the Turing
> > > > > architecture performance is going to suffer for the foreseeable
> > future.
> > > > > The hope I can offer is that the Ampere chips on the horizon appear
> > to
> > > > > resume an upward trend in the compute capacity of a single card, so
> > in
> > > > time
> > > > > simulations will again start to get faster.
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > > On Thu, May 28, 2020 at 2:26 PM Thomas Zeiser <thomas.zeiser.fau.de>
> > > > wrote:
> > > > >
> > > > > > On Wed, May 27, 2020 at 08:35:38PM +0200, Thomas Zeiser wrote:
> > > > > > > Hi Dave,
> > > > > > >
> > > > > > > please send me your SSH public key. I'll come back tomorrow with
> > > > > > > further instructions.
> > > > > >
> > > > > > you have to connect with SSH as w17p0001 to port 22622 of
> > > > > > grid.rrze.uni-erlangen.de
> > > > > > e.g. ssh -4 -p 22622 w17p0001.grid.rrze.uni-erlangen.de
> > > > > >
> > > > > > That should give you a shell on "testfront1". There, you can use
> > e.g.
> > > > > > srun -w medusa --time=10:0:0 --pty /bin/bash
> > > > > > to get an interactive job on the node "medusa" which hosts the
> > GPUs.
> > > > > >
> > > > > > CUDA, etc. are only installed on "medusa". Both testfront1 and
> > > > > > medusa can directly access data from the internet (through NAT).
> > > > > >
> > > > > > While you have a job running on medua, you can also SSH to medusa.
> > > > > > Once the job ends, all procces are kill. Thus, if you want to use
> > > > > > "screen", run it on testfront1.
> > > > > >
> > > > > > $HOME has a quota of 10 GB; $WORK of 333 GB.
> > > > > >
> > > > > >
> > > > > > Best
> > > > > >
> > > > > > thomas
> > > > > >
> > > > > > > Best
> > > > > > >
> > > > > > > thomas
> > > > > > >
> > > > > > > On Wed, May 27, 2020 at 02:29:58PM -0400, David Cerutti wrote:
> > > > > > > > This sounds like a great plan. I am about to test amber18 and
> > > > amber20
> > > > > > on a
> > > > > > > > local machine in another lab. If I can get access to the
> > server
> > > > with a
> > > > > > > > range of different Turing GPUs I can start to look at how your
> > > > problem
> > > > > > > > takes place.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > >
> > > > > > > > Dave
> > > > > > > >
> > > > > > > >
> > > > > > > > On Wed, May 27, 2020 at 9:08 AM Thomas Zeiser <
> > > > thomas.zeiser.fau.de>
> > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi Dave,
> > > > > > > > >
> > > > > > > > > On Wed, May 27, 2020 at 07:54:32AM -0400, David Cerutti
> > wrote:
> > > > > > > > > > I cannot make a meaningful test on an RTX-2080Ti because
> > the
> > > > card
> > > > > > I have
> > > > > > > > > > access to are not sufficiently powered to give the right
> > > > numbers.
> > > > > > I see
> > > > > > > > > > about a 20% degradation relative to what Ross was able to
> > get.
> > > > > > Ditto for
> > > > > > > > > > an RTX-6000, which is nearly as fast as a V100 despite
> > having
> > > > 20%
> > > > > > too
> > > > > > > > > > little power feeding it.
> > > > > > > > >
> > > > > > > > > we could provide you temporary access to our HPC systems to
> > > > support
> > > > > > > > > you in investigating the prossible performance degradation.
> > > > > > > > >
> > > > > > > > > I'd could either offer one host with four different
> > Turing-based
> > > > > > > > > GPUs (Geforce 2070 Super, 2080 Super, Quadro RTX 5000, and
> > 6000)
> > > > or
> > > > > > > > > a node with 4x Geforce 2080Ti.
> > > > > > > > >
> > > > > > > > > Both systems are running Ubuntu 18.04. Cuda toolkits 9.0 up
> > to
> > > > 10.2
> > > > > > > > > are installedi together with driver 440.64.00.
> > Persistence-Mode
> > > > is
> > > > > > > > > enabled on all GPUs. cmake/3.11.1 would also be available as
> > > > > > > > > module.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Best
> > > > > > > > >
> > > > > > > > > thomas
> > > > > > > > >
> > > > > > > > > > Dave
> > > > > > > > > --
> > > > > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > > > > thomas.zeiser.fau.de
> > > > > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > > thomas.zeiser.fau.de
> > > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > >
> > > > > > --
> > > > > > Dr.-Ing. Thomas Zeiser, HPC Services
> > > > > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg (FAU)
> > > > > > Regionales Rechenzentrum Erlangen (RRZE)
> > > > > > Martensstra?e 1, 91058 Erlangen, Germany
> > > > > > Tel.: +49 9131 85-28737, Fax: +49 9131 302941
> > > > > > thomas.zeiser.fau.de
> > > > > > https://www.rrze.de/hpc & https://hpc.fau.de
> > > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 2
> > > > > Date: Thu, 28 May 2020 21:33:01 -0400
> > > > > From: David A Case <david.case.rutgers.edu>
> > > > > Subject: Re: [AMBER] Simulating pyridine in water TIP3P
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <
> > > > 20200529013301.ljprvlrh2piy3nob.vpn-client-172-16-9-226.rutgers.edu>
> > > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > > >
> > > > > On Thu, May 28, 2020, Debarati DasGupta wrote:
> > > > >
> > > > > >I faced this error in equilibration step. Should I have a smaller
> > cut
> > > > value?
> > > > > >Cutoff list exceeds largest sphere in unit cell!!
> > > > >
> > > > > No: you need to have a bigger system. When a side of the periodic
> > box
> > > > > gets to be less than about 20 Ang., it gets to be too small for
> > Amber to
> > > > > handle, since Amber was designed and optimized for larger periodic
> > > > > cells.
> > > > >
> > > > > You may be able to get away with setting skinnb to 1 (instead of its
> > > > > default value of 2). That will allow you to go to slightly smaller
> > > > > boxes. But it would be rather dangerous to reduce the cutoff value
> > to
> > > > > anything below 8 Ang: we cut off Lennard-Jones interactions at "cut",
> > > > > and 8 Ang. is already on the edge of being to small.
> > > > >
> > > > > By far the simplest fix is to just use more water molecules in your
> > > > > original setup.
> > > > >
> > > > > ....dac
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 3
> > > > > Date: Thu, 28 May 2020 23:57:59 -0400
> > > > > From: Kenneth Huang <kennethneltharion.gmail.com>
> > > > > Subject: Re: [AMBER] Tool to calculate CSP and NOE for DNA
> > trajectory?
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <
> > > > CALeh7kALqvra6YccT-Sp4J7sMPJA37ArLhizviAkuUHjsEdrxw.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Hi Christina,
> > > > >
> > > > > Thanks a lot for the insight and script! That more or less covers for
> > > > what
> > > > > I wanted to do NOE and CSP wise, and LAMORD should more or less fill
> > in
> > > > the
> > > > > gap that the protein CSP softwares I found weren't able to do.
> > > > >
> > > > > Best,
> > > > >
> > > > > Kenneth
> > > > >
> > > > > On Thu, May 28, 2020 at 8:42 AM Christina Bergonzo <
> > cbergonzo.gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi Kenneth,
> > > > > >
> > > > > > I do not know of any stand alone tools that will calculate NMR
> > > > observables
> > > > > > from a trajectory.
> > > > > > I regularly do this without too much hassle using a combination of
> > > > bash/awk
> > > > > > scripting and Cpptraj/shifts.
> > > > > > I also back out NOE distances from distance restraints - if you
> > want to
> > > > > > predict NOEs using a trajectory, that's a different question (see
> > > > Henriksen
> > > > > > et al. JPCB, dx.doi.org/10.1021/jp400530e), but also distance
> > based.
> > > > > >
> > > > > > If you look at the Cpptraj distance command, there is an option for
> > > > > > evaluating a distance as an NOE.
> > > > > > I write a script that takes my atoms of interest from whatever
> > > > experimental
> > > > > > file format I have, and formats them into the distance command:
> > > > > >
> > > > > > distance d0 :1.H1' :1.H4' type noe bound 0.0 bound 7.0 out
> > > > > > dist/noe.val.0.dat
> > > > > > ....
> > > > > > distance d50 :6.H5'' :6.H6 type noe bound 0.0 bound 7.0 out
> > > > > > dist/noe.val.50.dat
> > > > > > analyze statistics all out noe.dat
> > > > > >
> > > > > > The last part dumps analysis of each distance into a file (noe.dat)
> > > > > > containing initial and final values, avg and standard deviation,
> > 1/r^6
> > > > > > averages, # of violations, etc.
> > > > > > Example output:
> > > > > >
> > > > > > STATISTICS :1.H1' and :1.H4'
> > > > > > AVERAGE: 3.0492 (0.2559 stddev)
> > > > > > INITIAL: 3.0944
> > > > > > FINAL: 3.2662
> > > > > > NOE SERIES: S < 2.9, M < 3.5, W < 5.0, blank otherwise.
> > > > > > |SMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM|
> > > > > > NOE < 7.00 for 100.00% of the time
> > > > > > NOE <r^-6>^(-1/6)= 2.9650
> > > > > > #Violations: Low= 0 High= 0 Total= 0
> > > > > > Rexp= 7.0000 <Violation>= -4.0350
> > > > > >
> > > > > > < 2.5 2.5-3.5 3.5-4.5 4.5-5.5 5.5-6.5 > 6.5
> > > > > > -------------------------------------------------------
> > > > > > %occupied | 2.4 | 95.1 | 2.5 | | | |
> > > > > > average | 2.402 | 3.051 | 3.611 | | | |
> > > > > > stddev | 0.084 | 0.223 | 0.103 | | | |
> > > > > > -------------------------------------------------------
> > > > > > __________________________________________________________________
> > > > > >
> > > > > > For chemical shifts for nucleic acids, I use shifts for protons,
> > and
> > > > > > there's larmor-D for proton and carbon shifts.
> > > > > > And, I go through a similar procedure, where I look at the
> > experiment
> > > > to
> > > > > > see what's be deposited, use shifts to calculate those values from
> > > > PDBs (I
> > > > > > have found you'll need to rename 5' and 3' ends to their
> > non-terminal
> > > > > > counterparts i.e., C3 to C), and then calculate for each frame and
> > > > average.
> > > > > >
> > > > > > Good luck!
> > > > > > -Christina
> > > > > >
> > > > > > On Wed, May 27, 2020 at 7:48 PM Kenneth Huang <
> > > > kennethneltharion.gmail.com
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi all,
> > > > > > >
> > > > > > > A general question- does anyone know of tools (assuming there
> > isn't a
> > > > > > > combined suite) for calculating CSP or NOEs from a trajectory? I
> > know
> > > > > > > there's SPARTA+ and shiftX2 for protein CSPs for proteins, but
> > with
> > > > DNA
> > > > > > all
> > > > > > > I've seen is the NMR option in Gaussian, which seems
> > prohibitively
> > > > > > > expensive.
> > > > > > >
> > > > > > > Likewise for NOEs I know of MD2NOE but haven't ever used it in
> > > > context of
> > > > > > > DNA, and other than back-calculating from the distance
> > restraints, I
> > > > was
> > > > > > > just wondering if there had been any other options in cpptraj?
> > > > > > >
> > > > > > > Best,
> > > > > > >
> > > > > > > Kenneth
> > > > > > > --
> > > > > > > Ask yourselves, all of you, what power would hell have if those
> > > > > > imprisoned
> > > > > > > here could not dream of heaven?
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > -----------------------------------------------------------------
> > > > > > Christina Bergonzo
> > > > > > Research Chemist
> > > > > > Biomolecular Measurement Division, MML, NIST
> > > > > > -----------------------------------------------------------------
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Ask yourselves, all of you, what power would hell have if those
> > > > imprisoned
> > > > > here could not dream of heaven?
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 4
> > > > > Date: Fri, 29 May 2020 05:53:03 +0000
> > > > > From: Gustaf Olsson <gustaf.olsson.lnu.se>
> > > > > Subject: Re: [AMBER] Small molecules paramters
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID: <EDDA8042-177F-409D-9875-76E4A5AA9EF2.lnu.se>
> > > > > Content-Type: text/plain; charset="utf-8"
> > > > >
> > > > > According to the fifth information webpage
> > > > >
> > > > > ?Amber-compatible parameters can also be generated, although
> > Amber-style
> > > > force field files are not output (users can convert though with
> > parmed)?
> > > > > - http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
> > > > >
> > > > > It should be very possible. If it is advisable, I suspect that
> > depends
> > > > on the quality of generated parameters.
> > > > >
> > > > > Best regards
> > > > > // Gustaf
> > > > >
> > > > >
> > > > > On 28 May 2020, at 14:47, Athena N <athena.nas01.gmail.com<mailto:
> > > > athena.nas01.gmail.com>> wrote:
> > > > >
> > > > > Hi all,
> > > > >
> > > > > I want to know if it advisable to use any other force fields than
> > gaff
> > > > for
> > > > > small molecules like some indole and pyridine systems.? If we
> > generate
> > > > some
> > > > > parameters using fftk (force field tool kit), could we use those and
> > do
> > > > the
> > > > > simulation in AMBER?
> > > > >
> > > > > Thank you all
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 5
> > > > > Date: Fri, 29 May 2020 02:25:00 -0400
> > > > > From: Eduardo Mayo <eduardomayoyanes.gmail.com>
> > > > > Subject: Re: [AMBER] adding hydrogen to pdbqt ligand files
> > > > > To: amber.ambermd.org
> > > > > Message-ID:
> > > > > <CAFVrw=SeTENo9zGCZO3vHbQ=
> > > > ruZGs8HFYVJNv6WYqY2yaMwxyw.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Hi!
> > > > > I recommend:
> > > > > 1 convert to .mol file using babel (with and without -h) and check
> > if the
> > > > > tautomeric state is the desired.
> > > > > 2 if 1 didn't work then covert to smarts or smiles( so if you got a
> > > > > tautomeric state with local charge the smarts/smiles will have this
> > > > > information) . Use rdkit to covert smiles/smarts to rdkit.Mol and add
> > > > then
> > > > > the hydrogen. Chem.Embedded the molecule so you have a 3D model. The
> > read
> > > > > the mol file using Chem.MolFromMolFile. Align (you may need find the
> > > > mcse)
> > > > > the molecule obtained from smiles to the molecule obtained from the
> > mol
> > > > > file.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Message: 3
> > > > > Date: Tue, 28 Apr 2020 21:15:36 +0000 (UTC)
> > > > > From: Marawan Hussien <marawanhussain.yahoo.com>
> > > > > Subject: [AMBER] adding hydrogen to pdbqt ligand files
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID: <1174479232.1819345.1588108536730.mail.yahoo.com>
> > > > > Content-Type: text/plain; charset=UTF-8
> > > > >
> > > > > Is there is a standard leap command to add hydrogen atoms to
> > non-polar
> > > > > atoms (carbons) only during system building? I am preparing a
> > > > > protein-ligand system for MD from pdbqt protein-ligand complex and
> > do not
> > > > > want to change the ligand tautomeric state.? I tried rdkit, obabel,
> > > > chimera
> > > > > but every tool I tried will add hydrogen to the entire molecule, not
> > > > carbon
> > > > > atoms only? Any suggestion?
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 6
> > > > > Date: Fri, 29 May 2020 02:30:20 -0400
> > > > > From: David Cerutti <dscerutti.gmail.com>
> > > > > Subject: [AMBER] Amber20 Performance on RTX (Turing): known problems,
> > > > > with a patch forthcoming
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <
> > > > CAEmzWj2pfjPxJg0-O+th+VyMcBsjFhqERfM0AJDtxZAzps6v2Q.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Dear Users,
> > > > >
> > > > > As has been shared on this listserv, many users are finding that
> > Amber20
> > > > is
> > > > > not as fast on Turing architectures for PME simulations as Amber18.
> > The
> > > > > source of this problem has now been identified, and indeed it affects
> > > > much
> > > > > more than just Turing, but the 15-20% slowdown seen on Turing is
> > merely
> > > > the
> > > > > most severe case.
> > > > >
> > > > > The slowdown itself does NOT reflect any bugs or issues that would
> > > > > necessitate repeating experiments. The problem, rather, is that some
> > > > > future-proofing that our collaborators at NVIDIA kindly performed
> > for us
> > > > > has led to more GPU effort in synchronization. The benefit of this
> > is
> > > > > that, come CUDA 11 and the new Ampere chipset, pmemd.cuda is already
> > > > > prepared to run on the cards (at a substantially greater speed than
> > is
> > > > > currently possible with a V100, which in my view competes with
> > RTX-6000
> > > > for
> > > > > top dog). However, legacy chipsets that do not need to perform the
> > > > > synchronization required for CUDA 11 to work properly will suffer in
> > > > > performance.
> > > > >
> > > > > Contrary to what I warned yesterday afternoon, a fix is possible and
> > we
> > > > > already have it. A compiler-specific directive will create separate
> > code
> > > > > paths for the various chipsets and mask out the synchronization
> > where it
> > > > is
> > > > > not needed, recovering the Amber18 performance while still keeping
> > the
> > > > code
> > > > > in a state that is ready for the next architecture.
> > > > >
> > > > > I would like to thank Scott Legrand, Peng Wang, and others at NVIDIA
> > who
> > > > > contributed either to the future-proofing or the short-term recovery
> > > > > effort. As you sit at home preparing your new simulations, please
> > enjoy
> > > > > some ice cream or other simple treat while you await the forthcoming
> > > > patch
> > > > > that will put Amber20 back where it should be on the benchmarks.
> > > > >
> > > > > Sincerely,
> > > > >
> > > > > Dave Cerutti
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 7
> > > > > Date: Fri, 29 May 2020 16:29:44 +0800 (GMT+08:00)
> > > > > From: "Gao J" <21919039.zju.edu.cn>
> > > > > Subject: [AMBER] questions for mdgx-virtual site
> > > > > To: amber.ambermd.org
> > > > > Message-ID: <59110ff3.e289d.1725f8d21aa.Coremail.21919039.zju.edu.cn
> > >
> > > > > Content-Type: text/plain; charset=UTF-8
> > > > >
> > > > > Hello
> > > > >
> > > > > I want to perform mix-solvent MD in amber and to prevent aggregation
> > > > ofbenzene probes, I need to set virtual sites on the probes with L-J
> > > > repulsions between themselves merely. My parameters for &rule were as
> > > > follows and I got an error said "ReadEPRuleFile >> Error. Extra point
> > name
> > > > unspecified." So I wonder what the correct format of "epname" or "atom"
> > > > required. What's more, I am a little confused if any parameters needed
> > for
> > > > "excl[1,2]".
> > > > >
> > > > > I really appreciate for your help!
> > > > >
> > > > > &rule
> > > > >
> > > > > frame[1,2]: C1 C4
> > > > >
> > > > > epname: VSB
> > > > >
> > > > > atom: VSB
> > > > >
> > > > > style: 1
> > > > >
> > > > > excl[1,2]
> > > > >
> > > > > v12: 0.5
> > > > >
> > > > > Sig: 21
> > > > >
> > > > > eps: 0.01
> > > > >
> > > > > residue: UNK
> > > > >
> > > > > &end
> > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 8
> > > > > Date: Fri, 29 May 2020 05:42:42 -0400
> > > > > From: David Cerutti <dscerutti.gmail.com>
> > > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <
> > > > CAEmzWj1n-DX_UodrWv9srcjbPRDDb03vmabfuFwTo5Rau6SO3w.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > OK, so good evening! mdgx is not going to be FAST simulator but if
> > you
> > > > > just need to get a system running a few thousand (or even million)
> > steps
> > > > of
> > > > > MD then it'll do fine. I am working right now to enable this virtual
> > > > site
> > > > > functionality in pmemd and also tleap, so with luck it'll be
> > possible to
> > > > > create more interesting molecular models in the standard MD engines
> > soon.
> > > > >
> > > > > For the &rule namelist, it's... a &namelist, just like &cntrl or
> > &ewald
> > > > in
> > > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > > technically the Fortran standard, but it gets things pretty well and
> > lets
> > > > > you have some flexibility. I would try writing this first:
> > > > >
> > > > > &rule
> > > > > frame1 = "C1",
> > > > > frame2 = "C2",
> > > > > epname = "VSB",
> > > > > style = 1,
> > > > > v12 = 0.5,
> > > > > sig = 2.1,
> > > > > eps = 0.05,
> > > > > residue = "UNK",
> > > > > &end
> > > > >
> > > > > In your input, you have lots of colon punctuation (:) that mdgx won't
> > > > know
> > > > > how to parse (nor will sander or pmemd). And I've written the above
> > in
> > > > > shorthand. There are aliases for all those keywords if you find one
> > or
> > > > the
> > > > > other easier to remember ("sig" can also be "Sigma"), but the
> > keywords
> > > > ARE
> > > > > case-sensitive. The "epname" keyword actually has four aliases,
> > > > "epname",
> > > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard
> > there.)
> > > > >
> > > > > The excl2 keyword is an ATTEMPT at a glaring problem with some extra
> > > > > points: if they're right on the middle of a bond, or equally close to
> > > > more
> > > > > than one real atom in general, how do we count their exclusions?
> > (This
> > > > is a
> > > > > reason that one of the experienced force field developers I work with
> > > > > demands that all of these extra points be close to their ONE parent
> > atom
> > > > > (which I refer to in mdgx as frame1) to make a tight association.) By
> > > > > definition, an extra point is 1:1 to its parent atom, so all
> > non-bonded
> > > > > exclusions of the frame1 atom will be inherited by the extra point.
> > But
> > > > if
> > > > > you specify excl2, it's going to take your frame2 atom and say that
> > the
> > > > > extra point is also 1:1 to that. Ditto for excl3, so the extra
> > point is
> > > > > accumulating more and more exclusions, atoms that it will not count
> > > > > interactions with.
> > > > >
> > > > > This makes me realize that I need to document this part of the code
> > a bit
> > > > > better, specifically in the onboard manual. There are descriptions
> > for
> > > > all
> > > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the command
> > > > line.
> > > > > But not for &rule...
> > > > >
> > > > > Happy to help more, and you are not the first to make use of mdgx to
> > > > create
> > > > > some very unorthodox (not unusual, just not what the typical programs
> > > > > simulate) molecular models. It HAS been done before, and not just
> > by me
> > > > :-)
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > > >
> > > > > > Hello
> > > > > >
> > > > > > I want to perform mix-solvent MD in amber and to prevent
> > aggregation
> > > > > > ofbenzene probes, I need to set virtual sites on the probes with
> > L-J
> > > > > > repulsions between themselves merely. My parameters for &rule were
> > as
> > > > > > follows and I got an error said "ReadEPRuleFile >> Error. Extra
> > point
> > > > name
> > > > > > unspecified." So I wonder what the correct format of "epname" or
> > "atom"
> > > > > > required. What's more, I am a little confused if any parameters
> > needed
> > > > for
> > > > > > "excl[1,2]".
> > > > > >
> > > > > > I really appreciate for your help!
> > > > > >
> > > > > > &rule
> > > > > >
> > > > > > frame[1,2]: C1 C4
> > > > > >
> > > > > > epname: VSB
> > > > > >
> > > > > > atom: VSB
> > > > > >
> > > > > > style: 1
> > > > > >
> > > > > > excl[1,2]
> > > > > >
> > > > > > v12: 0.5
> > > > > >
> > > > > > Sig: 21
> > > > > >
> > > > > > eps: 0.01
> > > > > >
> > > > > > residue: UNK
> > > > > >
> > > > > > &end
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 9
> > > > > Date: Fri, 29 May 2020 05:49:46 -0400
> > > > > From: David Cerutti <dscerutti.gmail.com>
> > > > > Subject: Re: [AMBER] questions for mdgx-virtual site
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <CAEmzWj3n5=
> > > > jWdmadVwoi-DVsCWC90bGnhNQ7440eWsoDWEPLnQ.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Another note: if you are trying to simulate a mixture of two
> > solvents and
> > > > > finding that the two molecular models do not want to stay mixed,
> > this is
> > > > a
> > > > > well-known problem in many models. If you want to just have virtual
> > > > sites
> > > > > (extra points) sticking out of the benzene to push benzenes away from
> > > > each
> > > > > other, that's one way to do it but it sounds extremely "staged"
> > shall we
> > > > > say. It would be like you've contrived the model and getting any
> > useful
> > > > > properties out of it would be a hard sell. I'm not actually sure you
> > > > could
> > > > > do this--mdgx is going to see the LJ parameters you assign to the
> > virtual
> > > > > sites and then try to apply the reigning LJ combining rule to
> > determine
> > > > how
> > > > > they interact with other atoms. So they'd interact with ALL other
> > atoms
> > > > of
> > > > > the simulation according to Lorentz-Berthelot combining rules, I
> > expect,
> > > > > not just other virtual sites.
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > > On Fri, May 29, 2020 at 5:42 AM David Cerutti <dscerutti.gmail.com>
> > > > wrote:
> > > > >
> > > > > > OK, so good evening! mdgx is not going to be FAST simulator but
> > if you
> > > > > > just need to get a system running a few thousand (or even million)
> > > > steps of
> > > > > > MD then it'll do fine. I am working right now to enable this
> > virtual
> > > > site
> > > > > > functionality in pmemd and also tleap, so with luck it'll be
> > possible
> > > > to
> > > > > > create more interesting molecular models in the standard MD engines
> > > > soon.
> > > > > >
> > > > > > For the &rule namelist, it's... a &namelist, just like &cntrl or
> > > > &ewald in
> > > > > > the sander and pmemd programs. The parser I wrote for it is not
> > > > > > technically the Fortran standard, but it gets things pretty well
> > and
> > > > lets
> > > > > > you have some flexibility. I would try writing this first:
> > > > > >
> > > > > > &rule
> > > > > > frame1 = "C1",
> > > > > > frame2 = "C2",
> > > > > > epname = "VSB",
> > > > > > style = 1,
> > > > > > v12 = 0.5,
> > > > > > sig = 2.1,
> > > > > > eps = 0.05,
> > > > > > residue = "UNK",
> > > > > > &end
> > > > > >
> > > > > > In your input, you have lots of colon punctuation (:) that mdgx
> > won't
> > > > know
> > > > > > how to parse (nor will sander or pmemd). And I've written the
> > above in
> > > > > > shorthand. There are aliases for all those keywords if you find
> > one
> > > > or the
> > > > > > other easier to remember ("sig" can also be "Sigma"), but the
> > keywords
> > > > ARE
> > > > > > case-sensitive. The "epname" keyword actually has four aliases,
> > > > "epname",
> > > > > > "atom", "AtomName", and "ExtraPoint." (I went a little overboard
> > > > there.)
> > > > > >
> > > > > > The excl2 keyword is an ATTEMPT at a glaring problem with some
> > extra
> > > > > > points: if they're right on the middle of a bond, or equally close
> > to
> > > > more
> > > > > > than one real atom in general, how do we count their exclusions?
> > (This
> > > > is a
> > > > > > reason that one of the experienced force field developers I work
> > with
> > > > > > demands that all of these extra points be close to their ONE parent
> > > > atom
> > > > > > (which I refer to in mdgx as frame1) to make a tight association.)
> > By
> > > > > > definition, an extra point is 1:1 to its parent atom, so all
> > non-bonded
> > > > > > exclusions of the frame1 atom will be inherited by the extra point.
> > > > But if
> > > > > > you specify excl2, it's going to take your frame2 atom and say
> > that the
> > > > > > extra point is also 1:1 to that. Ditto for excl3, so the extra
> > point
> > > > is
> > > > > > accumulating more and more exclusions, atoms that it will not count
> > > > > > interactions with.
> > > > > >
> > > > > > This makes me realize that I need to document this part of the
> > code a
> > > > bit
> > > > > > better, specifically in the onboard manual. There are descriptions
> > > > for all
> > > > > > mdgx &namelists available by typing, i.e. mdgx -PARAM on the
> > command
> > > > line.
> > > > > > But not for &rule...
> > > > > >
> > > > > > Happy to help more, and you are not the first to make use of mdgx
> > to
> > > > > > create some very unorthodox (not unusual, just not what the typical
> > > > > > programs simulate) molecular models. It HAS been done before, and
> > not
> > > > just
> > > > > > by me :-)
> > > > > >
> > > > > > Dave
> > > > > >
> > > > > >
> > > > > > On Fri, May 29, 2020 at 4:30 AM Gao J <21919039.zju.edu.cn> wrote:
> > > > > >
> > > > > >> Hello
> > > > > >>
> > > > > >> I want to perform mix-solvent MD in amber and to prevent
> > aggregation
> > > > > >> ofbenzene probes, I need to set virtual sites on the probes with
> > L-J
> > > > > >> repulsions between themselves merely. My parameters for &rule
> > were as
> > > > > >> follows and I got an error said "ReadEPRuleFile >> Error. Extra
> > > > point name
> > > > > >> unspecified." So I wonder what the correct format of "epname" or
> > > > "atom"
> > > > > >> required. What's more, I am a little confused if any parameters
> > > > needed for
> > > > > >> "excl[1,2]".
> > > > > >>
> > > > > >> I really appreciate for your help!
> > > > > >>
> > > > > >> &rule
> > > > > >>
> > > > > >> frame[1,2]: C1 C4
> > > > > >>
> > > > > >> epname: VSB
> > > > > >>
> > > > > >> atom: VSB
> > > > > >>
> > > > > >> style: 1
> > > > > >>
> > > > > >> excl[1,2]
> > > > > >>
> > > > > >> v12: 0.5
> > > > > >>
> > > > > >> Sig: 21
> > > > > >>
> > > > > >> eps: 0.01
> > > > > >>
> > > > > >> residue: UNK
> > > > > >>
> > > > > >> &end
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> AMBER mailing list
> > > > > >> AMBER.ambermd.org
> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 10
> > > > > Date: Fri, 29 May 2020 08:40:59 -0500
> > > > > From: Timothy Schutt <tschutt7.gmail.com>
> > > > > Subject: [AMBER] igb for non-aqueous solvent?
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <CAGGi8+gfyC=aCWfrDO+8oEpWCOzyTBnGQqUja4yv=
> > > > 9w1o2Bm5A.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Hi Amber Folks!
> > > > >
> > > > > Is it an okay approximation to use igb=1 and extdiel=*dielectric
> > value*
> > > > to
> > > > > represent a non-aqueous solvent implicitly?
> > > > >
> > > > > I would like to investigate some surface binding interactions of a
> > > > > non-aqueous solvent but the solvents are too viscous to get decent
> > > > sampling
> > > > > in a reasonable time frame so my thought was to use 2D umbrella
> > sampling
> > > > > across the surface sites using just one explicit solvent molecule
> > with
> > > > the
> > > > > rest being implicit. In each solvent system I would use the
> > different one
> > > > > explicit solvent and the approrpiate external dielectric for that
> > solvent
> > > > > in bulk. Would that be an accurate enough approach to provide
> > reliable
> > > > > trends of mapping different solvents interactions with the surface?
> > > > >
> > > > > Any advice is greatly appreciated, Thanks!
> > > > >
> > > > > -Tim
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 11
> > > > > Date: Fri, 29 May 2020 09:46:58 -0500
> > > > > From: Pinky Mazumder <pmazumder67.gmail.com>
> > > > > Subject: Re: [AMBER] cellulose chain
> > > > > To: AMBER Mailing List <amber.ambermd.org>, Lachele Foley
> > > > > <lf.list.gmail.com>
> > > > > Message-ID:
> > > > > <
> > > > CAFoDHbjw9EqX4ewswc+agnru_2pRMZR2kssyXzUjW0u5x7GRQw.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Thank you.
> > > > >
> > > > > I can place the chains parallel to each other. After that, I need to
> > see
> > > > > the h-bond interaction between the polymers. For that I ran the
> > > > simulations
> > > > > with energy minimization, heating and production MD.
> > > > >
> > > > > Even after, I do not see the H-Bond. To do so, what process I need to
> > > > > follow?
> > > > >
> > > > > Thank you.
> > > > >
> > > > > Sincerely,
> > > > > Pinky
> > > > >
> > > > > On Sat, May 16, 2020 at 4:33 AM Lachele Foley <lf.list.gmail.com>
> > wrote:
> > > > >
> > > > > > When you copy the chains, they have exactly the same x,y,z
> > > > > > coordinates. In other words, they are right on top of each other.
> > > > > >
> > > > > > You will need to use the translate and/or transpose commands to put
> > > > > > them into the proper relative geometries.
> > > > > >
> > > > > > On Fri, May 15, 2020 at 11:53 PM Pinky Mazumder <
> > pmazumder67.gmail.com
> > > > >
> > > > > > wrote:
> > > > > > >
> > > > > > > Please discard my previous message.
> > > > > > >
> > > > > > >
> > > > > > > Thank you so much for your cordial response.
> > > > > > >
> > > > > > >
> > > > > > > I can copy the chain using this command and the numbers of
> > atoms are
> > > > > > > increasing.
> > > > > > >
> > > > > > >
> > > > > > > However, I am not able to see the two chains together in vmd or
> > in
> > > > the
> > > > > > > xleap using the edit command.
> > > > > > >
> > > > > > >
> > > > > > > Could you please help me in this regard?
> > > > > > >
> > > > > > >
> > > > > > > Thank you again.
> > > > > > >
> > > > > > > Sincerely,
> > > > > > > Pinky
> > > > > > >
> > > > > > > On Fri, May 15, 2020 at 10:51 PM Pinky Mazumder <
> > > > pmazumder67.gmail.com>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Thank you so much for your cordial response.
> > > > > > > >
> > > > > > > >
> > > > > > > > But, I can show the two chains together using vmd. I can
> > copying
> > > > the
> > > > > > chain
> > > > > > > > because the numbers of atoms are increasing.
> > > > > > > >
> > > > > > > >
> > > > > > > > However, I am not able to see the two chains together.
> > > > > > > >
> > > > > > > >
> > > > > > > > Could you please help me in this regard?
> > > > > > > >
> > > > > > > >
> > > > > > > > Thank you again.
> > > > > > > >
> > > > > > > > Sincerely,
> > > > > > > >
> > > > > > > > On Fri, May 15, 2020 at 10:09 PM Lachele Foley <
> > lf.list.gmail.com>
> > > > > > wrote:
> > > > > > > >
> > > > > > > >> First, you need to know the geometric relationships between
> > the
> > > > > > > >> chains. The relationships will differ based on the source of
> > the
> > > > > > > >> cellulose.
> > > > > > > >>
> > > > > > > >> In leap, you can use:
> > > > > > > >>
> > > > > > > >> chain2 = copy chain1
> > > > > > > >>
> > > > > > > >> to make a copy of a chain.
> > > > > > > >>
> > > > > > > >> Then, once you know the relative geometries, you can use
> > translate
> > > > > > > >> and/or transform to position the chains properly with respect
> > to
> > > > each
> > > > > > > >> other.
> > > > > > > >>
> > > > > > > >> Alternatively, find an experimentally-determined structure,
> > such
> > > > as an
> > > > > > > >> X-ray or cryo-EM structure.
> > > > > > > >>
> > > > > > > >> Also consider contacting Dr. Jodi Hadden. She can probably
> > help
> > > > you,
> > > > > > > >> but she's pretty busy with other stuff, so you might have to
> > be
> > > > > > > >> patient.
> > > > > > > >>
> > > > > > > >> On Fri, May 15, 2020 at 1:01 PM Pinky Mazumder <
> > > > pmazumder67.gmail.com
> > > > > > >
> > > > > > > >> wrote:
> > > > > > > >> >
> > > > > > > >> > Hi David,
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > Thank you for your response.
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > I have been able to make the polymer of cellulose. But I
> > need
> > > > > > multiple
> > > > > > > >> > chains together.
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > Could you please suggest how can I replicate the same
> > polymer
> > > > chain
> > > > > > or
> > > > > > > >> can
> > > > > > > >> > I build the multiple number of polymer chain together?
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > Is there any specific tutorial or command that I need to
> > follow?
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > Thank you.
> > > > > > > >> >
> > > > > > > >> >
> > > > > > > >> > Kind regards,
> > > > > > > >> >
> > > > > > > >> > Pinky
> > > > > > > >> >
> > > > > > > >> > On Sun, Apr 5, 2020, 12:20 PM David A Case <
> > > > david.case.rutgers.edu>
> > > > > > > >> wrote:
> > > > > > > >> >
> > > > > > > >> > > On Thu, Apr 02, 2020, Pinky Mazumder wrote:
> > > > > > > >> > > >
> > > > > > > >> > > >I want to build a chain of cellulose. So when I am
> > trying to
> > > > do
> > > > > > this
> > > > > > > >> by
> > > > > > > >> > > >using foo sequence command.
> > > > > > > >> > > >
> > > > > > > >> > > > It says that '' Error : sequence : ILLEGAL UNIT named
> > Glc''.
> > > > > > > >> > >
> > > > > > > >> > > Are you inside tleap at this point? If so, execute the
> > "list"
> > > > > > > >> command,
> > > > > > > >> > > and see if Glc is one of the units listed. If not, you
> > would
> > > > > > need to
> > > > > > > >> > > somehow load the units you want.
> > > > > > > >> > >
> > > > > > > >> > > Carbohydrates are discussed in Chap. 3 of the Amber
> > Reference
> > > > > > Manual:
> > > > > > > >> > > you might see if that would help.
> > > > > > > >> > >
> > > > > > > >> > > If this is not a tleap error, then please give more
> > details
> > > > about
> > > > > > > >> > > exactly what you mean by "using foo sequence command".
> > > > > > > >> > >
> > > > > > > >> > > ...thx...dac
> > > > > > > >> > >
> > > > > > > >> > >
> > > > > > > >> > > _______________________________________________
> > > > > > > >> > > AMBER mailing list
> > > > > > > >> > > AMBER.ambermd.org
> > > > > > > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >> > >
> > > > > > > >> > _______________________________________________
> > > > > > > >> > AMBER mailing list
> > > > > > > >> > AMBER.ambermd.org
> > > > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >>
> > > > > > > >>
> > > > > > > >>
> > > > > > > >> --
> > > > > > > >> :-) Lachele
> > > > > > > >> Lachele Foley
> > > > > > > >> CCRC/UGA
> > > > > > > >> Athens, GA USA
> > > > > > > >>
> > > > > > > >> _______________________________________________
> > > > > > > >> AMBER mailing list
> > > > > > > >> AMBER.ambermd.org
> > > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >>
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Pinky, Sharmi
> > > > > > > > AL,US
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Pinky, Sharmi
> > > > > > > AL,US
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > :-) Lachele
> > > > > > Lachele Foley
> > > > > > CCRC/UGA
> > > > > > Athens, GA USA
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Pinky, Sharmi
> > > > > AL,US
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 12
> > > > > Date: Fri, 29 May 2020 12:20:56 -0400
> > > > > From: Gustavo Seabra <gustavo.seabra.gmail.com>
> > > > > Subject: Re: [AMBER] Small molecules paramters
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <CAO4guEKk=
> > > > 2u1gnzrdBp8hSCDsV5yaN2Q52Muip+SW3_QcOW_hg.mail.gmail.com>
> > > > > Content-Type: text/plain; charset="UTF-8"
> > > > >
> > > > > Although it is possible to convert parameters to AMBER *format*, so
> > they
> > > > > can be read by AMBER, this is not the ideal. Bear in mind that the MD
> > > > force
> > > > > fields rely on a fine balance between charges and force constants
> > > > > obtained from multiple calculations, and that each force field
> > "flavor"
> > > > > uses a different methodology to obtain those parameters. So,
> > ideally, you
> > > > > will want to use for your small molecule the same methodology that
> > was
> > > > used
> > > > > to derive parameters for the rest of the system, or at least have
> > some
> > > > > indication that the parameters are compatible. GAFF (ad GAFF2) have
> > been
> > > > > developed with that in mind, so their parameters are, in principle,
> > > > > compatible with the Amber force fields. If you get the parameters
> > from
> > > > > other sources, make sure you do some extra testing.
> > > > >
> > > > > All the best,
> > > > > --
> > > > > Gustavo Seabra.
> > > > >
> > > > >
> > > > > On Thu, May 28, 2020 at 8:47 AM Athena N <athena.nas01.gmail.com>
> > wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I want to know if it advisable to use any other force fields than
> > gaff
> > > > for
> > > > > > small molecules like some indole and pyridine systems.? If we
> > generate
> > > > some
> > > > > > parameters using fftk (force field tool kit), could we use those
> > and
> > > > do the
> > > > > > simulation in AMBER?
> > > > > >
> > > > > > Thank you all
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Message: 13
> > > > > Date: Fri, 29 May 2020 12:32:06 -0400
> > > > > From: David A Case <david.case.rutgers.edu>
> > > > > Subject: Re: [AMBER] cellulose chain
> > > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > > Message-ID:
> > > > > <
> > > > 20200529163206.k2wr3wlvv2kcwtee.vpn-client-172-16-9-226.rutgers.edu>
> > > > > Content-Type: text/plain; charset=us-ascii; format=flowed
> > > > >
> > > > > On Fri, May 29, 2020, Pinky Mazumder wrote:
> > > > > >
> > > > > >I can place the chains parallel to each other. After that, I need
> > to see
> > > > > >the h-bond interaction between the polymers. For that I ran the
> > > > simulations
> > > > > >with energy minimization, heating and production MD.
> > > > > >
> > > > > >Even after, I do not see the H-Bond. To do so, what process I need
> > to
> > > > > >follow?
> > > > >
> > > > > I guessing you need a better starting structure. Do the chains move
> > > > > much during the simulation? If there are no inter-chain hydrogen
> > bonds
> > > > > in the starting structure, it may difficult to get them to form just
> > > > > with MD, even if the H-bonded structure has a lower free energy.
> > > > >
> > > > > You may be able to get some good ideas, plus a feeling for how mobile
> > > > > your chains are, by looking at the trajectories you have.
> > Generally, MD
> > > > > simluations sample configurations close to the starting point, and
> > > > > either long simulations or advanced sampling methods are required to
> > > > > find quite different structures.
> > > > >
> > > > > If you know what H-bonds you would like to form, you could add
> > > > > restraints (called "NMR" restraints in Amber lingo, for historical
> > > > > reasons) that will pull the H-bond donor and acceptor atoms to an
> > > > > H-bonding geometry.
> > > > >
> > > > > ....good luck...dac
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
> > > > > End of AMBER Digest, Vol 3017, Issue 1
> > > > > **************************************
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > End of AMBER Digest, Vol 3019, Issue 1
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> >
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 1 Jun 2020 10:00:00 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] igb for non-aqueous solvent?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200601140000.4ute4l66memde4qb.diajbutler.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Fri, May 29, 2020, Timothy Schutt wrote:
> >
> >Is it an okay approximation to use igb=1 and extdiel=*dielectric value* to
> >represent a non-aqueous solvent implicitly?
>
> "okay" is a tough thing to answer here. Some points to consider:
>
> 1. Non-aqueous solvents are charactized by more than just a dieletric
> constant; with gb, changing extdiel changes way in which Coulomb
> interactions are screened. This does not capture all of the differences
> between solvent.
>
> 2. Amber's GB models have not been tested (much) with other solvents.
> Maybe I'm unaware of some of this work, and I hope others will chime in
> with appropriate references. So, as far as I know, one doesn't know if
> your proposed scheme will yield "reliable trends" for different
> solvents. On top of this, you are proposing a kind of hydbrid model,
> with one explicit solvent molecule and the rest being implicit; this is also
> likely to require careful testing.
>
> That said, this is research, after all. It might well work, and has
> some reasonable physics in it, especially if your solvent molecules are
> fairly small and rigid. n-octanol as a solvent would be stretch, since
> it is floppy and has both polar and non-polar parts. It's a balance
> between how much time your have and how accurate your results need to
> be.
>
> An alternative would be to stick with explicit solvation, and use some
> enhanced sampling method (replica exchange, self-guilded Langevin,
> perhaps one of the GaMD variants) to address the viscosity problem.
>
> ....good luck....dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 1 Jun 2020 09:34:27 -0500
> From: Timothy Schutt <tschutt7.gmail.com>
> Subject: Re: [AMBER] igb for non-aqueous solvent?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGGi8+gShN9MztdGmJTu+eR7OTcQD+xHm9PW02912Jj6pmjjLQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks for the insights Dr. Case!
>
> On Mon, Jun 1, 2020 at 9:00 AM David A Case <david.case.rutgers.edu> wrote:
>
> > On Fri, May 29, 2020, Timothy Schutt wrote:
> > >
> > >Is it an okay approximation to use igb=1 and extdiel=*dielectric value* to
> > >represent a non-aqueous solvent implicitly?
> >
> > "okay" is a tough thing to answer here. Some points to consider:
> >
> > 1. Non-aqueous solvents are charactized by more than just a dieletric
> > constant; with gb, changing extdiel changes way in which Coulomb
> > interactions are screened. This does not capture all of the differences
> > between solvent.
> >
> > 2. Amber's GB models have not been tested (much) with other solvents.
> > Maybe I'm unaware of some of this work, and I hope others will chime in
> > with appropriate references. So, as far as I know, one doesn't know if
> > your proposed scheme will yield "reliable trends" for different
> > solvents. On top of this, you are proposing a kind of hydbrid model,
> > with one explicit solvent molecule and the rest being implicit; this is
> > also
> > likely to require careful testing.
> >
> > That said, this is research, after all. It might well work, and has
> > some reasonable physics in it, especially if your solvent molecules are
> > fairly small and rigid. n-octanol as a solvent would be stretch, since
> > it is floppy and has both polar and non-polar parts. It's a balance
> > between how much time your have and how accurate your results need to
> > be.
> >
> > An alternative would be to stick with explicit solvation, and use some
> > enhanced sampling method (replica exchange, self-guilded Langevin,
> > perhaps one of the GaMD variants) to address the viscosity problem.
> >
> > ....good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
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>
>
> End of AMBER Digest, Vol 3020, Issue 1
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Received on Mon Jun 01 2020 - 18:30:02 PDT
