Re: namd question

From: Peter Freddolino (
Date: Wed Dec 27 2006 - 12:56:13 CST

Hi Regina,
if you're just looking to recenter things as a visualization and
analysis aid, you should look into the VMD script align_frames.tcl
(included in the tutorials, and discussed previously on this list at I
assume this is what you meant, since recentering the box during
simulation doesn't really have a physical meaning.

" politr" wrote:
> Dear NAMD developers
> I'm trying to find some function that allows to recenter my peptide in
> a PBC every couple of frames during the simulation. I want to be able
> to preclude center of mass motion due to external forces as random
> noise in Langevin dynamics. Another option is to use some tool (VMD
> for example) in order be able to recenter the peptide after
> minimization in the trajectory. I hope you will be able to help me
> with this issue. I will appreciate it very much. Looking for your
> answer as soon as possible. Thank you very much for your help
> Regina

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