AW: a problem about pbc in a namd trajectory

From: Norman Geist (
Date: Mon Aug 26 2013 - 03:44:14 CDT


If you don't want to see how your molecule was drifting through the box, try
the "-center" and "-centersel" options.


pbc wrap -all -center com -centersel "your molecule"

To additionally prevent the solvent from being split when single atoms
crossed the bounds, try "-compound"

Therefore the full command:

pbc wrap -all -compound res -center com -centersel "your molecule"

Please do that wrapping carefully as it can change results, depending on
what kind of analyzations you're doing.

Best wishes

Norman Geist.

> -----UrsprĘ╣ngliche Nachricht-----
> Von: [] Im
> Auftrag von ???
> Gesendet: Montag, 26. August 2013 09:44
> An: namd-l
> Betreff: namd-l: a problem about pbc in a namd trajectory
> Dear professor,
> We simulated a pentamer protein with NAMD. I am confused about that
> some part of the pemtamer fluctuated in and out of the box. I dealed
> with pbctools in vmd and failed. The command used are at below.
> package require pbctools
> pbc readxst xstfile
> pbc box_draw
> pbc wrap -all
> The unrecognizable code was displayed when I opened the processed
> trajectory using VMD.
> Would you tell me the reason and the solution?

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:34 CST