Re: About Membrane anlysis

From: Jeffrey Potoff (
Date: Wed Dec 18 2013 - 09:50:03 CST

On 12/18/2013 10:09 AM, Vidhya Sankar wrote:
> I am Doing Membrane Simulation. I have Completed The Simlation . Then
> I would Like to Analyse
> The Following Properties of Membrane
> 1)Deutrium order Parameter
> 2) Density of membrane
> 3) Area per Lipid Group
> 4)Bilayer Thickness
> 5) Lateral Diffusion'
> Is Ther is Any Tools or Scripts Availabele in Namd
> Thanks In Advance

There are no tools in NAMD for this. Some of the properties you have
listed are trivial to calculate with some rudimentary knowledge of TCL
and/or shell scripting.

There are tools available, but they generally require some expertise to
use. SIMtoEXP allows one to compare simulation to experimental x-ray
and neutron scattering data:

Using Google will turn up a basic TCL script for calculating order

Jeffrey J. Potoff               
Associate Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202

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