From: Axel Kohlmeyer (
Date: Wed Oct 15 2008 - 11:20:33 CDT

On Wed, 15 Oct 2008, Ryan Pavlovicz wrote:

RP> Can VMD calculate the velocities of the atoms of a trajectory? I am missing
RP> a restart file for AMBER, and would like to recreate the file to include
RP> velocity information. Thanks,

vmd currently does not read or store velocity information
and thus will not write it out.

you still would be facing the problem, that the reconstruction
of velocities is a bit tricky as well (you could use finite differences
or some equivalent higher order polynomial scheme) and would have
to be programmed in tcl or python script as well.

it is probably much easier to just reinitialize the velocities,
either randomly or by running a few steps NVE and then scaling
up to the desired value. the impact of any of this on a system
compared to continuing perfectly from the restart is generally
much smaller than what people think.


RP> ryan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.