From: Jeffrey Potoff (jpotoffx_at_gmail.com)
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:
http://sourceforge.net/projects/simtoexp/
Using Google will turn up a basic TCL script for calculating order
parameter:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-5378/orderparam2.tcl
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================
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