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
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