From: Albert (
Date: Thu Nov 15 2012 - 01:37:27 CST


   I find that VMD doesn't interpret well for my system. The place of my
protein becomes messy and I cannot analyze anything for MD results. Here
is a screenshot for it:

as we can see, the system is not in the PBC BOX, I try to use the command:

  pbc wrap -orthorhombic -shiftcenterrel {1 0 0}

and the problem is still there.

  I am just wondering how can I center my protein in the pbc box?

thank you very much