[gmx-users] Number of degrees of freedom for generating velocities

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 11 18:54:20 CET 2008

Esteban Vöhringer wrote:
>   Hi,
> I was looking into the code, how the velocities are generated in grompp, 
> once the option genvel is used in the .mdp file.
> I don't understand why the number of degrees of freedom which are used 
> to calculate the scaling factor for the random velocities is 3N and not 
> 3N-Nc ( Nc= Number of constraitns; N=Number of atoms).
> is there some special reason?
because the constraints are not taking into account during vel. 
generation. before the first MD step the constraints are applied and the 
temperature is approximately correct.
> Tank you in advance for your help
> Esteban
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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