[gmx-users] Excessive compute time using PME

[Jordi Camps]

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
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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