[gmx-users] Excessive compute time using PME

[Jordi Camps]

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.

Sincerely,

-- 
Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
UPC-CIRI
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