membrane protein simulation lipid bilayer question

From: Tian Li (
Date: Wed Oct 02 2013 - 19:48:35 CDT

Dear namd users,

I'm using the NAMD membrane protein simulation tutorial as a guidance to
set up my own membrane protein simulation system. Everything looks
reasonable until the second step of minimization and equilibration which is
put a harmonic constraint on protein, and also apply the tcl script to keep
certain water molecule from going through membrane. After about 100000
steps simulation, the membrane lipids seems to moving away from protein,
I'm wondering what could be the cause of this? the periodic boundary
condition? or something else. Especially in the tutorial it applies Margin
3 to allow large volume fluctuation, would this cause the problem? I attach
a figure of my system, so you can see the lipids are spreading out. Hope
that some one can give me some suggestions to modify my system.

Thanks in advance!
Initial setup:

after minimization and equilibration:


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:44 CST