[gmx-users] Free energy calculations and speed problems

[Justin A. Lemkul]

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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 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/

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