AW: moving out of the box

From: Norman Geist (
Date: Thu Feb 13 2014 - 14:24:53 CST

In VMDs console

pbc wrap -all -compound res -center com -centersel "protein or nucleic"

or similar

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Ariel Talavera Perez
> Gesendet: Donnerstag, 13. Februar 2014 16:57
> An:
> Betreff: namd-l: moving out of the box
> Hello,
> I just ran 0.5 us MD us of a protein dimer in complex with DNA in a
> water box. Unfortunately I did not restrain the neither the translation
> nor the rotation of the complex. In several frames part of the complex
> moved out of the water box. This makes that sometimes one of the
> monomers is gone from the water box, and the same monomer but from the
> neighbour cell appears.
> Is there anyway to fix this issue for the MD I already ran? I mean, how
> can I get the "right" complex in all the frames?
> Thanks a lot in advanced
> Cheers,
> Ariel

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:28 CST