Re: Evaluating kinetic energy from a modified DCD file

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Apr 08 2009 - 16:57:01 CDT

Thanks Peter for your suggestion but I am doing modal decomposition for the
DCD. So if I poceeed as you suggested I have to do also modal decomposition
for the velocity DCD file . I dont think that the modes of the velocity file
have the same physical meaning as the modes of the DCD file.
That is why I couldnt use it in the first place.
I may be mistaken. Correct me if I am.
Best,
Mert

On Wed, Apr 8, 2009 at 11:15 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> 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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