[gmx-users] Free energy calculations and speed problems

[Justin A. Lemkul]

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.
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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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========================================

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/

========================================