From: Norman Geist (
Date: Wed Mar 02 2016 - 01:41:01 CST


What about:


pbc wrap –center com –centersel „one central atom of you membrane“ –compound
res -all

pbc wrap –center com –centersel “your whole membrane” –compound res –all


Why two times? The first will make sure the membrane is always complete. As

“–center com” for the full membrane will otherwise be uneffective, think
about it. The second wrap will finally wrp you membrane to the center of the
unit cell, which should be less jumpy than the 1st wrap result. If you
already have a wrapped trajectory, do before above steps:


pbc join connected


Good luck.


Norman Geist


Von: [] Im Auftrag von
Deng, Jinxia (Nancy)
Gesendet: Dienstag, 1. März 2016 16:03
Betreff: vmd-l: pbc to keep membrane in center


Hi All,


I have a simple membrane system with water on both sides. The MD trajectory
of 50ns (by NAMD) shows the membrane keep moving slowly till top of the


I played with the pbc plugin, trying various combinations including unwrap
and join etc... But still could not keep membrane in its central position as
I want.


I am wondering whether anyone would like to share with me your step-wise pbc


Looking forward to hearing from you.