[gmx-users] bad contact distance.

[David van der Spoel]

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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