[gmx-users] PBC dodecahedron

meetnahren at yahoo.com meetnahren at yahoo.com
Mon Mar 23 11:10:36 CET 2009

Dear Gromacs Users,

I am having some trouble in viewing my molecule in VMD as a protein in dodecahedron.
I did the following

1.  trjconv -f promd.trr -o nojump.xtc -s promd.tpr -pbc nojump

2.  trjconv -f nojump.xtc -s promd.tpr -o mdcenter.xtc -ur compact -pbc mol -center -boxcenter tric

I have run my simulation for 12 ns (of a protein dimer ). I see the box remain octahedron till about 5 ns after that the sides of the dodecahedron becomes unequal.
i tried -pbc atom/whole etc, but does not help.
Any advice on the issue will be truly helpful. 


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