[gmx-users] Excessive compute time using PME

Jordi Camps jcamps at lsi.upc.edu
Fri May 13 18:05:24 CEST 2005

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?

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.


Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
c/. Jordi Girona 1-3              
Modul C6-E201                     Tel.  : 934 011 650
E-08034 Barcelona                 Fax   : 934 017 014
Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu

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