[gmx-users] The same lysozyme.pdb file under 3.3.3 and 4.0.5 version

Chih-Ying Lin chihying2008 at gmail.com
Fri Sep 4 08:04:32 CEST 2009

I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under
16 nodes.

Simply, lysozyme.pdb + water.
There is no problems (errors) with 3.3.3 version.

However, with 4.0.5 version, the same lysozyme pdb file with the same
simulation condition.
except mdrun -pd with minimisation steps

Relaxation of solvent and hydrogen atom positions: Position restrained MDIt
shows the following errors.
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 3651

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

How does it happen?

Thank you
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