VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 04 2006 - 18:24:15 CST

Hi,
  At present VMD doesn't read or store velocity information from the
trajectory file formats it supports. This means that the only velocity
data you'd have to work with would have to be read in by your own script
from some external file of some sort. The details will depend greatly
on what software your reading simulation results from, and so it would
be helpful if you described that more fully. In principle you'd save
the scalar velocity value for each atom in the "User" field for that
atom for each timestep in your trajectory, and then you'd use the
color by "User" method to display the structure colored by velocity.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 03, 2006 at 05:41:07PM -0600, yuhl wrote:
> Hi
> I am currently doing some research on lattice structure MD simulations. I want to animate the result to observe the varies of the kinetic energy for each atom and each time step. So I tried to color each atom according to its velocity for each frame. But I dont know how to realize it with VMD. Could anybody give me a clue? Thanks a lot
> Hualong 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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