From: Axel Kohlmeyer (
Date: Mon Jul 05 2010 - 17:02:53 CDT

On Mon, Jul 5, 2010 at 4:59 PM, Ardy Davari <> wrote:
> Hi,
> Are there any scripts available to color a charmm dcd/psf by kinetic energy?

how should this work?
the dcd file only stores atom coordinates
and the psf file only has the topology.

> If not, what's the best way to go about producing one?

you cannot show what is not there.

at best, you could do a crude approximation by computing
the difference of atom coordinates between two subsequent
frames, dividing it by the time that has passed, square it, and
multiply by the half the mass to get the per atom kinetic energy.


> Best,
> Ardy Davarifar

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.