[gmx-users] PBC dodecahedron

[meetnahren at yahoo.com]

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



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090323/f2f84a29/attachment.html>