[gmx-users] bad contact distance.

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 12 13:02:06 CET 2002

On Tue, 2002-11-12 at 10:53, Nguyen Hoang Phuong wrote:
> Dear All,
> I have one gro file containing both velocities and coordinates of
> the solute and the water molecules. I would like remove bad contact
> distances between the waters and the solute. I have performed either the
> energy minimization or run MD for a few ps with the solute are
> frozen. However, in two cases the velocities of the solute in the output
> file are set to zero. The problem is that I still need the velocities
> and the coordinates of the solute in the gro file for the simulations
> Does anyone know how to do that? Thanks a lot in advance.
grompp can generate velocities for you. Set gen_vel to yes and gen_temp
to 300 K (or whatever you want). This is OK, since you need to
equilibrate with position restraints anyway.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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