[gmx-users] bad contact distance.

[Anton Feenstra]

Nguyen Hoang Phuong wrote:
> 
> > 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).

You can paste the velocities into your .gro file using a text editor.
Or, maybe easier, combine the solute coordinates + velocities (which
have not changed since they were frozen) from your input .gro file
with the solvent coordinates (and velocities?) from your output .gro
file.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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