Membrane Simulations

From: Anshu Bhatia (
Date: Tue Oct 14 2008 - 14:05:55 CDT

Hi Namd users,

I am trying to simulate
(a)POPE membrane and
(b) a gramicidin channel in POPE,
similar to the one described in protocol. However, I need clarifications on
a number of points.
Here is what I am doing stepwise and my doubts in every step.

(1) Get a 100 by 100 patch from vmd membrane plugin.

(2) Solvate it more using the solvate plugin and remove waters which are
inside the lipid bilayer.

(3) Minimize for some steps

(4) Hold everything constant but for waters and run a NVT

The purpose of these 4 steps is to get the additional water from solvate to
its right density. But I see the water
height rising towards the middle which does not seem right. What could be
the reason for this, and how should
I modify my protocol to get a good equilibrated membrane?
  After reading a few threads in the archive I found out that people are
melting lipid tails to get lipids to their experimental
density and then run a constant area simulation.

(5)For equilibrating only the membrane/water system itself should melting
tails precede the MD simulation of whole system.
If so in what ensemble should the melting done.

I think the assumption here is that the whole membrane behaves uniformly
after it has been brought to its ideal density values.
Again my question is the following:

(6) If I want to see how far in space the protein affects the membrane,
should I still be using a constant area patch? How
should I proceed if I want to observe the variances in lipid properties
across the span of the membrane.


Anshu Bhatia
Graduate Student,
Tri I Computational Biology Program ,
Weill Cornell Graduate School,

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