VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed May 12 2010 - 04:55:06 CDT

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On 05/12/2010 10:37 AM, Mühlbacher, Markus wrote:
> I have a problem with the pbc wrap command. I did a membrane simulation (POPC bilayer) where the membrane moved away from the center of the unit cell during the simulation Thus I am trying to re-center my trajectory so that the membrane stays in the middle of the unit cell. For that reason I used the command:
>
> pbc wrap -centersel “resname POPC” -center com -all

> This does put the membane back into middle of the unit cell, but draws quite strange bonds through the whole unit cell. So my question would be how to re-center a piece of membrane for each frame of the trajectory correctly?
> Thank you in advance for your help!

If I assume correctly that the different lipids have distinct resids,
then what you want to do should work with

pbc wrap -centersel "resname POPC" -center com -compound res -all

which tells "pbc wrap" to keep together residues.

Olaf
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