From: Olaf Lenz (
Date: Mon May 26 2014 - 02:38:58 CDT


2014-05-25 20:18 GMT+02:00 Shailesh Pandey <>:

> Dear Dr. Olaf,
> I am Shailesh Kr. Pandey, a PhD student at Jawaharlal Nehru University,
> New Delhi, India. I have done a MD simulation of a Protein-Peptide complex
> using NAMD 2.9 with charmm force field with PBC. Now I see that during
> simulation when complex moves towards any face of the PBC box If peptide is
> pushed outside the box in this case it is wrapped and in central PBC box
> but it appears from the opposite face of the PBC box, and it is now not in
> binding site of the protein. But actually it should be in the binding site
> because the observed case is just result of the PBC effect. I tried so
> solve this problem, I looked and tried pbctools plugin in vmd by you, but
> could not solve the problem. Now I am not sure whether pbctools can solve
> it. If it is possible, please let me know the sequence of commands to be
> executed, I would be thankful to you.
> I am attaching pdb psf and a dcd with 16 frames in which 1st and last are
> normal cases and others with fliped peptide.
> Thanks & Regards
> Shailesh Kr. Pandey
> SCIS, JNU, New Delhi, India

Please pose your questions on the mailing list. Like that, other people can
reply to your questions, and furthermore the replies are archived so that
others can profit from them. A copy of this mailing goes to the VMD mailing

The simplest solution to your problem is the command "pbc unwrap", which
will make your trajectory continuous and remove wrapping jumps. Note that
this also means that atoms will walk out of the central image.

If you want a cleaner solution, then you should identify some atoms that
belong to the binding pocket and use a selection of these atoms as the
center of the wrapping box in the command. In your system, this command
gave good results:

  pbc wrap -center com -centersel "index 4145" -sel "segname P2"

Atom "4145" is some oxygen atom in the binding pocket. The command wraps
the segment P2 (i.e. the peptide) into the periodic image that is centered
at atom 4145.


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607