VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 15 2008 - 11:11:02 CDT

Hi,
  You can't really compute missing velocities from thin air. The only way
you'd be able to produce a velocity restart file is if you had stored
every timestep your trajectory, which is quite unusual.
I don't know if AMBER has a way to re-initialize the velocities
given some temperature set point, but something like that may be
a better way of doing it than trying to reconstruct what they were
at the end of the last run.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 15, 2008 at 11:18:50AM -0400, Ryan Pavlovicz wrote:
> Can VMD calculate the velocities of the atoms of a trajectory? I am missing
> a restart file for AMBER, and would like to recreate the file to include
> velocity information. Thanks,
>
> ryan 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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