Re: Recentering the box on target molecule and wraping

From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Mon Sep 11 2006 - 11:56:59 CDT

Forget this message - I made it if GROMACS tools.

Have a nice day to all
Arturas Z.

>
>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.
>
>

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