[EMAIL PROTECTED] wrote:
Dear users,
There is an option in .mdp named comm_mode, which deals with the transition
and rotation of the molecule being simulated. I want to know why the transition
and rotation happens during the simulation. Can any one suggest me any
reading material where in I can find how the dynamics is performed internally.
thanks in advance
@Article{Harvey98a,
author = {S. C. Harvey and R. K. Z. Tan and T. E. Cheatham},
title = {The flying ice cube: Velocity rescaling in molecular
dynamics leads to violation of energy equipartition},
journal = {J. Comp. Chem.},
year = 1998,
volume = 19,
pages = {726-740}
}
regards
Anwar
----------------------
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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