[gmx-users] box changes its shape !

[Mark Abraham]

On 30/01/2012 4:54 PM, Kowsar Bagherzadeh wrote:
> Dear gmx-users,
> Running MD, I faced a problem, after 1ps of modeling, the box changes 
> its shape from  dodecahedron to rhomboid cube! and as a result some 
> parts of  the protein gets out of the box. I fixed it with trjcon 
> command but keep comming up. Would you mind telling me where this 
> problem arise from?!

This sounds like normal behaviour. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark
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