[gmx-users] box changes its shape !

Kowsar Bagherzadeh kw_bagherzadeh at yahoo.com
Mon Jan 30 06:54:42 CET 2012

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?!
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