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
> -----原始邮件-----
> 发件人: amber-request.ambermd.org
> 发送时间: 2020-05-30 03:00:01 (星期六)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: 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
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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: 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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Received on Sat May 30 2020 - 19:30:01 PDT
