[gmx-users] bad contact distance.
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Tue Nov 12 13:38:22 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.
the problem is that I still need the old values of velocities of the
solute in the gro file. (which were generated for a special purpose).
> 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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