Re: Evaluating kinetic energy from a modified DCD file

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 08 2009 - 15:15:00 CDT

Try writing a velocity DCD
(http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node13.html#1360)

Peter

Mert Gür wrote:
> I have performed a molecular dynamic simulation in a waterbox. Using the
> dcd file I am doing modal decomposition on the cartesian coordinates .
> By keeping selected modes (for example only the first mode) I go back to
> the cartesian coordinates and generate a new dcd file.
> Using this new DCD file I am trying to evaluate the potential energies
> and the kinetic energies of the selected modes.
> If I am not mistaken , NAMD energy plugin gives me the potential energy
> with respect to this DCD file(atom coordinates).
> But to evaluate the kinetic energy, I was planning to use the
> coordinates of the previous and succesive time frames. Using this frames
> I was going to evaluate the velocity and hence the KE. Unfortunately in
> the light of the answer I received for my previous question I see that
> getting these subsequent time frames is not an easy job.
> This is the point where I am stuck now. Any suggestions about how to
> evaluate the kinetic energy will be appreciated.
> Best,
> Mert

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