[gmx-users] Free energy calculations and speed problems

[Michael Shirts]

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.