membrane constraints on thickness

From: Himanshu Khandelia (
Date: Thu Jan 25 2007 - 11:58:39 CST


I am equilibrating a protein in a membrane. The simulation box initially
has a larger area than the calculated area based on area per lipid, and
the cross sectional area of the protein.

In order to equilibrate it to the right area, I need to restrict the
thickness of the bilayer, while allowing the area to reduce gradually
under (preferably) NPT circumstances. Is there a harmonic potential in
NAMD that can be enforce upon the headgroups to keep their average
z-coordinate fixed ?

Thank you


Himanshu Khandelia
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics
University of Southern Denmark (SDU)
Odense M 5230, Denmark
Phone: +4565503510

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:19 CST