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
>
> > -----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
> > 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
> >
> >
> >
> >
> > ------------------------------
> >
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> >
> >
> > End of AMBER Digest, Vol 3017, Issue 1
> > **************************************
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Received on Sat May 30 2020 - 21:30:02 PDT
