Evaluating kinetic energy from a modified DCD file

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Apr 08 2009 - 14:33:05 CDT

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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