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

From: Daniel Roe <>
Date: Wed, 8 Jan 2014 09:23:08 -0700


If you want to calculate the mean squared displacement for a 'wrapped'
system, you can first use the 'unwrap' command in cpptraj/ptraj (which is
essentially the reverse of 'image' and will ensure your molecules take
continuous paths), followed by either the 'diffusion' command in
ptraj/cpptraj or the stfcdiffusion command in cpptraj (which is an
alternative to the traditional diffusion command written by Hannes

Hope this helps,


On Wed, Jan 8, 2014 at 12:45 AM, Vijay Manickam Achari <
> wrote:

> 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.
> Regards
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 08 2014 - 08:30:02 PST
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