[AMBER] calculating MSD by correcting the center-of-mass-motion

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Wed, 8 Jan 2014 07:45:07 +0000 (GMT)

Dear SIr,

I am doing bilayer simulation and I would like to calculate MSD (mean square displacement) for the lipids in the bilayer.

Since my simulation is quite long (~200ns), I have used flags like ntxo=1, iwrap=1, nscm=5000.

In the literature, ( for example J.Chem. Phys., Vol. 115, No. 10, 8 September 2001) indicated that before the MSD calculation the authors have corrected the center-of-mass motion in each layer before calculating. They used GROMACS.

Well, since I am using AMBER12, do I still need to do the correction for the center-of-mass motion in each layer before calculating the MSD in AMBER? If yes how do I do the correction? I could not find anything related to this in the manual.

Hope kindly I can get some explanation and help . 
Many thanks in advance.


Vijay Manickam Achari 
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
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Received on Wed Jan 08 2014 - 00:00:03 PST
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