VMD-L Mailing List

From: Mühlbacher, Markus (Markus.Muehlbacher_at_uk-erlangen.de)
Date: Wed May 12 2010 - 03:37:13 CDT

Dear VMD users,

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!

Best regards,
Markus Muehlbacher