[gmx-users] bad contact distance.

[Nguyen Hoang Phuong]

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.

Regards,

Phuong