Yes, what he said.
On Mon, May 19, 2008 at 3:00 PM, van Bemmelen <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> > Subject: [gmx-users] Free energy calculations and speed problems > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > 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@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
