[gmx-users] Excessive compute time using PME
spoel at xray.bmc.uu.se
Sat May 14 09:23:30 CEST 2005
On Sat, 2005-05-14 at 03:29 +0200, Jordi Camps wrote:
> 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:
Check the grid anyway, but the first steps are extra costly because you
turned on optimize_fft. Try it without.
> 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
> constraint_algorithm= shake
> 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
> -----Mensaje original-----
> 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.
> > 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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