From: Norman Geist (
Date: Wed Jan 28 2015 - 07:26:42 CST

Into VMD console/TK console:


pbc wrap -all -compound res -center com -centersel protein


Norman Geist.


Von: [] Im Auftrag von
Sourav Ray
Gesendet: Mittwoch, 28. Januar 2015 12:15
Betreff: vmd-l: Re-centering protein molecule




After running a NAMD simulation, when I run the .dcd file (with the
corresponding .psf), although the position of waterbox remains invariant.
The protein molecule fluctuates a lot, I would like to fix the center of the
protein molecule to the center of the box, can someone help me please.


Sourav Ray