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
