[gmx-users] Excessive compute time using PME

David spoel at xray.bmc.uu.se
Fri May 13 19:20:16 CEST 2005

On Fri, 2005-05-13 at 18:05 +0200, Jordi Camps wrote:
> Dear sirs,
> I'm trying to run some simulations with PME, but the time that them takes
> are unusually long.
> Finally I reduced the number of steps to compute to only two (2) steps and
> one system with about 20000 atoms takes about 140 seconds to compute
> (spending 98% of the time "solving PME"). But if I take out the
> coulombtype=PME parameter (so I simulate with a cut-off), the time needed
> for the same two steps is about 3 seconds.
> Adding PME calculus should increase the compute time, but not in this
> magnitude order.
> If I let the simulation run for more time, I get about 1500 steps in 12
> hours (approx.).
> Is this normal? Could it be a compilation problem? An uncorrected bug? A
> parameter definition problem?

Is your box nearly empty and very large? Or are you using a very fine
spaced grid?

> I can supply the .mdp and the other files if necessary.
> I've been simulating on one processor (in multiple processors behaves
> similarly). I'm using PBC too.
> Thanks for your help.
> Sincerely,
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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