Re: Evaluating kinetic energy from a modified DCD file

From: JT (jtibbitt_at_odu.edu)
Date: Wed Apr 08 2009 - 19:59:48 CDT

Mert,
Doing modal decomposition gives you both the eigenvalues (frequencies)
and their corresponding eigenvectors (modes). Then aren't the
individual modal velocities, obtained by just multiplying the two?
After all, an eigenvector represents the displacement and the
frequency the reciprocal of the time it takes for that displacement to
occur.
Jeff

On Apr 8, 2009, at 5:57 PM, Mert Gür wrote:

> 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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