[gmx-users] Free energy calculations and speed problems

[David Mobley]

Yes, what he said.

On Mon, May 19, 2008 at 3:00 PM, van Bemmelen
<J.J.M.vanBemmelen at student.tudelft.nl> wrote:
> Hi Justin,
>
> You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no)
> cutoffs.
>
> I'm not entirely sure why PME takes such a long time, but I can give a very
> wild guess. It may have something to do with the fact that, if I remember
> correctly, the Fourier transform of one (or a few) large charge spike(s) can
> only be represented to a certain precision by taking very high frequencies
> into account. Therefore the FFT has to calculate ridiculously long to reach
> the desired accuracy.
>
> Hope it helps,
> Jeroen
>
>
>
> Date: Mon, 19 May 2008 15:04:51 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: [gmx-users] Free energy calculations and speed problems
> To: gmx-users at gromacs.org
> Message-ID: <1211223891.4831cf53f0a46 at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
>
> Hi all,
>
> 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.
>
> -Justin
>
> _______________________________________________
> 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
>