[gmx-users] Free energy calculations and speed problems

Wed May 21 09:51:37 CEST 2008

Hi,

Note that there are proper options for this (no cut-off's):
ns_type = simple
pbc = none
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0

Berk.

> Date: Tue, 20 May 2008 12:45:35 -0700
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Free energy calculations and speed problems
> 
> Justin and Michael,
> 
> Just to clarify here, I don't think you want the "long cutoff in
> vacuum" scheme to give you the same results as the "PME in vacuum"
> scheme. That is, if you use PME in vacuum with a periodic box, you
> will be including copies of the long-range unscreened electrostatic
> interactions between your molecule and its periodic copies. Unless
> your box is gigantic, you will probably see significant contributions
> to the energy from these. I think for most ordinary vacuum
> calculations (i.e. comparing to a vacuum reference state for, say,
> hydration free energies) you don't want these contributions and your
> desired reference state is something more like the molecule in vacuum,
> with no cutoffs, but with no periodic copies. You can achieve that
> most easily by simply running in vacuum without pme but making the
> cutoffs huge enough to include all of the intramolecular interactions.
> Of course, for a protein this would probably be a bad idea for speed
> reasons, but for small molecules it can work well.
> 
> David
> 
> 
> On Tue, May 20, 2008 at 8:06 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> > Just to follow up - the cutoff scheme worked quite well.  It gave me energies
> > that were ~1% different from those of the PME calculation, which I think
> > compares quite well.  The 10-ps run I attempted now takes 3 seconds, instead of
> > 20 minutes.
> >
> > Thanks to everyone for the suggestions.
> >
> > -Justin
> >
> > Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> >
> >>
> >> Thanks to everyone for the insights.  I'll try running things with the cutoff
> >> and see how it goes.
> >>
> >> -Justin
> >>
> >> Quoting Michael Shirts <mrshirts at gmail.com>:
> >>
> >> > Hi, Justin-
> >> >
> >> > Have you considered -not- running PME in vacuo?  If you set your
> >> > cutoffs and rlist large enough, then you can just run with simple
> >> > cutoffs, and it should run -faaaast-.  Of course, you should compare
> >> > to the energy with PME -- if they are not equivalent, then you many
> >> > need to go back and check your PME parameters for accuracy.
> >> >
> >> > Best,
> >> > Michael
> >> >
> >> > > I'm running some free energy calculations (in vacuo and in solution) for
> >> a
> >> > set
> >> > > of molecules I am trying to parameterize.  All the molecules are fairly
> >> > small,
> >> > > about 30-35 atoms in each.  The solvated calculations go smoothly, and
> >> > rather
> >> > > quickly (~5 hr/ns on two nodes).  I am running into a problem when I do
> >> the
> >> > in
> >> > > vacuo calculations.  Since I am constraining all bonds, I am running
> >> things
> >> > on
> >> > > a local machine in the lab (single core AMD64 Opteron).  I get as far as
> >> > NVT
> >> > > equilibration (removing charges only) before I give up and kill it, since
> >> > it
> >> > > takes so long.  A 10-ps NVT run takes about 20 minutes, but that adds up
> >> to
> >> > > over 5 days for my 5-ns production run!  The machine is no slouch; I have
> >> > used
> >> > > it to run other small NVT/NPT/MD runs with good performance.  I get
> >> similar
> >> > > performance on another machine that is even faster (a single CPU of the
> >> > 2-CPU
> >> > > node on our supercomputer).  The installations of Gromacs on both are
> >> fine,
> >> > as
> >> > > far as I can tell, and both have been used extensively.
> >> > >
> >> > > I am using Gromacs version 3.3.3, and I have attached my .mdp file and
> >> the
> >> > tail
> >> > > end of my log file for reference.  If anyone notices anything obvious
> >> that
> >> > I'm
> >> > > doing wrong, I would be grateful if you pointed it out!  I see in the log
> >> > of
> >> > > the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU
> >> > > usage.  Is that indicative of any problem?
> >> > >
> >> > > Thanks for your attention.
> >> > _______________________________________________
> >> > gmx-users mailing list    gmx-users at gromacs.org
> >> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/search before posting!
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> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >>
> >>
> >>
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Graduate Research Assistant
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul at vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >>
> >> ========================================
> >> _______________________________________________
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> >>
> >
> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
> > _______________________________________________
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> >
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