msd calculation for lipid bilayers

From: cnu gromacs (
Date: Thu May 05 2011 - 14:22:24 CDT


I am looking to calculate mean square displacement of lipids, in a bilayer
simulation of 128 lipid molecules 64 in each layer.

After following some literature/mailing list, I am confused with the
calculation of MSD for lipid molecules

I understand from the literature that, I need to correct the MSD values for
Center of Mass motion (COM) of lipid bilayer or COM of the individual
monolayers? Is that right? I was wondering How do I do that using VMD ?
Any script is available for msd calculation of lipid bilayer?

I would appreciate if you can provide some input.


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