[gmx-users] refcoord-scaling

Chetan Mahajan chetanvm10 at gmail.com
Mon Mar 24 01:10:48 CET 2014

When 4 times lower timestep is used, simulation runs a bit longer, but does
crash after that.

On Sun, Mar 23, 2014 at 7:05 PM, Chetan Mahajan <chetanvm10 at gmail.com>wrote:

> 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!
> regards
> Chetan
> Errors:
> 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 up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> 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
> paper <http://dx.doi.org/10.1021/ct700301q>). 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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