VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Thu Nov 15 2012 - 01:37:27 CST

hello:

   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:

https://dl.dropbox.com/u/56271062/pbcbox.jpeg

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
best
Albert