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" <[EMAIL PROTECTED]>: > > Thanks to everyone for the insights. I'll try running things with the cutoff > and see how it goes. > > -Justin > > Quoting Michael Shirts <[EMAIL PROTECTED]>: > > > 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@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 > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
