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.
regards,
nahren
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