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

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> 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
> 
> Then,
> 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?
> Why?

Didn't I already answer such a question from you today?

Mark