[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

[WU Yanbin]

Hi, Mark,

Thanks for the reply.

As suggested, I tried a "water in vacuum" case. Initially the water droplet
is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the
simulation box. Everywhere else is just vacuum. The simulation box size is
8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water
molecules.

Such system is first equilibrated with "steep" option.

The "mdrun" simulation goes with no problem with parallel running on 32
cpus, even though there are occasionaly one or two water molecules move very
fast (Mean square displacement being 200 times fast than bulk water) in the
vacuum.

When I switch to 64 cpus, the error "X particles communicated to PME node Y
are more than a cell length out of the domain decomposition cell of their
charge group" appears.

Below is the parameter file I'm using.

------------------------------------
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000000

comm-mode                = Linear
nstcomm                  = 1
comm-grps                =

energygrps               =

nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.5

coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.5
epsilon-r                = 1

vdw-type                 = Cut-off ;Switch
rvdw-switch              = 1.0
rvdw                     = 1.5

fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

Tcoupl                   = nose-hoover
tc-grps                  = System
tau_t                    = 1.0
ref_t                    = 300

Pcoupl                   = no ;Parrinello-Rahman ;no ;berendsen
Pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 2008

constraints              = none
constraint-algorithm     = Lincs
Shake-SOR                = no
shake-tol                = 1e-04
lincs-order              = 4
lincs-warnangle          = 30

energygrp_excl           =
------------------------------------

Is there any parameters configuration wrong with the simulation? Or is there
any way to go around this error?

Any tip is appreciated.
Thank you.

Best,
Yanbin




>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 02 Dec 2010 17:24:18 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] How to suppress the error "X particles
>        communicated    to PME node Y are more than a cell length out of the
>        domain  decomposition cell of their charge group"
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CF73B92.40003 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2/12/2010 4:16 PM, WU Yanbin wrote:
> > Dear GMXers,
> >
> > I'm running a simulation of water contact angle measurement on top of
> > graphite surface.
> > Initially a water cubic box is placed on two-layer graphite surface
> > with the rest of the box being vacuum. The water droplet is relaxed
> > during the simulation to develop a spherical shape.
> >
> > An error of "X particles communicated to PME node Y are more than a
> > cell length out of the domain decomposition cell of their charge
> > group" was encountered.
> > And I have read the suggested solutions at the link below
> >
> http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
> .
> >
> > I guess the reason for this error in my case is because of the vacuum
> > such that the water molecules at the boundary of the droplet can move
> > fast. I have check the trajectory and the simulation is OK.
>
> I doubt the simulation is OK. This error message is one of several that
> can happen when the system is not well-enough conditioned for the MD to
> be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up.
> Here, you have atoms moving much faster than GROMACS was engineered to
> expect.
>
> You should be confident that a water drop in a vacuum, and your graphite
> surface are both stable on their own before you try the wetting simulation.
>
> >
> > For this situation, is there a way of suppressing this error? Or what
> > else can I do?
>
> Work out why it's poorly conditioned.
>
> Mark
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101226/09fe09d7/attachment.html>