[gmx-users] refcoord-scaling

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 24 10:16:49 CET 2014

On Mar 24, 2014 1:10 AM, "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
> with any of the following errors. Could anyone explain to me why is this
> happening

See the description of com. You didn't tell us what you were restraining,
so it's hard to help. But I can see multiple com of tio2 and PBC not
working well together, particularly if you box size is far from best.

> or when each of the options such as 'all', 'com' and 'no' is used?

When you really care about your starting position and need to equilibrate
in NPT.


> 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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