[gmx-users] refcoord-scaling

Chetan Mahajan chetanvm10 at gmail.com
Mon Mar 24 01:05:13 CET 2014

Dear all:

I am trying to get a simulation of water solvated titanium oxide running.
When 'all' option is used for refcoord-scaling, simulation runs ok.
However, when 'com' option is used for refcoord-scaling, simulation crashes
with any of the following errors. Could anyone explain to me why is this
happening or when each of the options such as 'all', 'com' and 'no' is used?

Thanks a lot!


X particles communicated to PME node Y are more than a cell length out of
the domain decomposition cell of their charge group

This is another way that mdrun tells you your system is blowing
In GROMACS version 4.0, domain decomposition was introduced to divide the
system into regions containing nearby atoms (for more details, see the
manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS 4
If you have particles that are flying across the system, you will get this
fatal error. The message indicates that some piece of your system is
tearing apart (hence out of the "cell of their charge group"). Refer
to the Blowing
Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up> page for
advice on how to fix this issue.

A charge group moved too far between two domain decomposition steps.

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