Re: [gmx-users] simulation with non-zero total charge

[Mark Abraham]

seunghwan lee wrote:
Mark,
Thanks for your comments.
Well, I am running simulations with or without neutralization to see the
effect of counter ions. The troubling simulations have messages like

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 1878999  vol min/aver 0.840! load imb.: force 18.6%

during the simulation and it has pretty big load imbalance. I am wondering
what is the meaning of "minimum cell size" in DD and how I can change it
manually.

See manual 3.17

Mark

--- On Fri, 12/11/09, Mark Abraham <mark.abra...@anu.edu.au> wrote:

From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] simulation with non-zero total charge
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Friday, December 11, 2009, 5:12 PM
seunghwan lee wrote:
Hi,

I am trying to simulate lipid bilayer with protein,
which has net positive
charge. If I run simulations after neutralizing, I
don't have any problem,
whether I use PME or reaction-field. But, when I try
to run it with net
positive charge using reaction-field, I got
domain-decomposition error
after 1800000 steps. In log file, I have

DD  load balancing is limited by minimum cell
size in dimension Z
DD  step 1878999  vol min/aver 0.840!
load imb.: force 18.6%
and the actual error message was

DD cell 0 0 5: Neighboring cells do not have atoms:
4484
DD cell 0 0 3: Neighboring cells do not have atoms:
4477

-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: domdec_con.c, line: 679

Fatal error:
DD cell 0 0 5 could only obtain 51 of the 52 atoms
that are connected via constraints from the neighboring
cells. This probably means your constraint lengths are too
long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or
lincs-order or use the -rcon option of mdrun.
My questions are:
(1) Is this error anything to do with the fact that
the system has net charge?

Potentially. Something's causing it to explode, but it can
be hard to tell why after the fact.

(2) How can I fix this with "-rcon" option? I don't
want to change LINCS order, etc.

Reading mdrun -h is the first port of call, however
changing this option is probably just fixing the symptoms,
not the cause.

(3) Is there any parameter that I need to be careful
when I simulate systems with non-zero net charge (especially
lipid system)?

With RF, I would have guessed that there's probably not
much to worry about. Probably nobody's studied it in any
detail, because it's so easy to neutralize, and so easy to
defend a neutral simulation as a realistic model of real
physics...

Mark
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