[gmx-users] Intial velocity

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 14 03:28:34 CEST 2006

Fan, Fenghui wrote:
> Dear all,
> For MD we need to get a initial velocity of the molecule randomly. Id the velocity linear vvelocity of the whole molecule or the vibration velovcity or some kinds of other velocity?
> In addition, as for the molecule is very large, there is the possibility that differeny parts of the protein has different velocity. Does this violate the randomly got velocity?
> Further more, for the MD system. it is in fact protein (can include ions and ligands) surrounded by water. Then it seems there will be no linaear movement of the whole molecule.
> I am looking forward to having these clarified.
> Best regards.
> Fenghui Fan
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this is described in the manual. the velocities are sampled according to 
a Maxwell-Boltzmann distribution at the temperature you request.

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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