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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