VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
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
using

“–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: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Deng, Jinxia (Nancy)
Gesendet: Dienstag, 1. März 2016 16:03
An: vmd-l_at_ks.uiuc.edu
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
unicell.

 

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
combinations...

 

Looking forward to hearing from you.

 

Nancy