VMD-L Mailing List

From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Mon Sep 11 2006 - 10:39:55 CDT

Hi,

Does anybody know how to recenter the box of trajectory from NAMD to certain molecule ? I have same molecule in my box and, naturaly, it is "flighing" all around in the box. I want to make it centered in my trajectory and wrapped.

Any clues or help ???

I tried to use pbcwrap: each frame I calculate center and cell dimensions. Later I calculate origin (take 1/2 length of box dimensions and substract it from {xyz} of my target molekule's center) for wraping the system. However I got very strange behaviour - does not help.

GROMACS's tools also has no help.

With best
Arturas Z.