From: Olaf Lenz (
Date: Mon Apr 04 2011 - 02:11:25 CDT


On 04/03/2011 11:34 PM, Mark M Huntress wrote:
> I am doing a classical MD trajectory of an organic molecule in a
> solvent box, and I am sampling frames (coordinates and velocities)
> from this MM trajectory to start new QMMM trajectories. For the
> frames that I am sampling, I am re-centering the solute in the
> solvent box (using pbc wrap -centersel {resid 1} -center com
> -compound res), and my concern is whether I can still use the
> velocities from the vel.dcd file. Will the coordinates and velocities
> be incompatible for any reason after I re-center? (for instance,
> reordering of solvent atoms or the velocities of some solvent atoms
> becoming in the wrong direction relative to the molecule?) Thanks,

The velocities should certainly be independent of the positions and
translational invariant. As long as you don't rescale the positions,
everything is safe.


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607