[gmx-users] Excessive compute time using PME

[David]

On Sat, 2005-05-14 at 03:29 +0200, Jordi Camps wrote:
> Hello!
> 
> 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:
> 	fourierspacing=0.12

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
> 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
> 
> -----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
> 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.
________________________________________________________________________
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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