[gmx-users] Excessive compute time using PME
jcamps at lsi.upc.edu
Sat May 14 03:29:58 CEST 2005
The box is full of waters (plus the protein) and not specially large. It is
a truncated octahedron box. The grid spacing is the standard:
Either way, this line is commented out.
The parameters are:
title = Simulation
cpp = /lib/cpp
integrator = md
dt = 0.002
nsteps = 2
nstlog = 500
nstxout = 500
nstenergy = 500
nstvout = 500
nstxtcout = 500
constraints = hbonds
pbc = xyz
;;;; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
;;;;tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.01325
;;;; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1
tc_grps = System
ref_t = 300
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
rlist = 1.0
optimize_fft = yes
;;;; Generate velocites is on at 300 K.
gen_vel = no
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
De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
nombre de David
Enviado el: viernes, 13 de mayo de 2005 19:20
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Excessive compute time using PME
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
> 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.
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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