On 27/12/2010 9:22 AM, WU Yanbin wrote:
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.
OK, that sounds like behaviour that might be expected... some molecules
evaporate. Check the trajectory to be confident this is the situation.
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.
The most plausible reason for this is that the above evaporated
molecules are moving so fast that they're doing what the error message
says - travelling more than width of a box in one integration step. The
DD implementation is predicated on that being impossible.
You might succeed by arranging for the largest possible internal DD cell
diameter, i.e. a 4x4x4 DD. mdrun -npme 0 might choose this, otherwise
use the hidden options to mdrun (use mdrun -hidden) to use that DD with
-npme 0.
Otherwise, you'll need to accept the fact that there are "engineering"
constraints on efficient parallelization algorithms, and not every
situation can be catered for. For example, a simulation of a bulk LJ
fluid would fail if you used so many processors that the cell diameter
was too small with respect to the distribution of particle speeds.
Mark
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.abra...@anu.edu.au
<mailto:mark.abra...@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@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4cf73b92.40...@anu.edu.au
<mailto:4cf73b92.40...@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
<http://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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
