[gmx-users] comm_mode

[David van der Spoel]

anwar at cdfd.org.in 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
> anwar.m1 at gmail.com
> -----------------------
> 
> -
> 
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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