VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Mar 23 2010 - 12:06:31 CDT

Hi all,

during my membrane only simulation the membrane has drifted to the most
positive side of the Z-Axis and most water is "above" the membrane.

Current Situation:
+ = Water
M = Membrane

 Z|
  |
  | +++++++++++
  | +++++++++++
  | +++++++++++
  | MMMMMMMMMMM
  | MMMMMMMMMMM
  | +++++++++++
--------------------->
  | X

Desired result:
 Z|
  |
  | +++++++++++
  | +++++++++++
  | MMMMMMMMMMM
  | MMMMMMMMMMM
  | +++++++++++
  | +++++++++++
--------------------->
  | X

I would like to recenter the membrane on the Z-Axis, so that I have an equal
amount of water above and below the membrane.

When i use
"pbc wrap -centersel "segname MEMB" -center centerofmass -compound res"
the water is wrapped correctly and I have an equal amount of water below and
above the protein, but the water is just shifted from top to bottom, so all
water what was wrapped in this process is now "out of the box" (I visualized
the box with "pbc box -center origin".

How can I recenter this to the box?
I played around with "pbc wrap" but couldn't figure out how to move it back
into the box.

Thanks for your help.
Kind regards
Bjoern 

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942