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
vjramana.gmail.com
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Received on Wed Jan 08 2014 - 00:00:03 PST
