**From:** JT (*jtibbitt_at_odu.edu*)

**Date:** Wed Apr 08 2009 - 22:04:20 CDT

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Mert,

I'm sorry, I was mistaken. The eigenvalue (Lk) of a principal mode is

not the same as the frequency (Wk) of the mode. They are related by:

Wk = sqrt [( kB*T) / Lk]

Also, I'm no expert on the subject, but I do understand a little

bit. And I'm not sure if the kinetic energy of a single mode derived

using Principal Component Analysis makes as much sense as it does in

classical Normal Mode Analysis (if it makes any sense in NMA for that

matter). It's because in PCA, the harmonic potential describing the

system is reconstructed only to satisfy some positional covariance

matrix (e.g. one obtained from an MD trajectory). The frequencies

thus obtained are much larger than they are in NMA. But surely in

certain settings, proper use can be made of the kinetic energies of

single PCA modes. And if you are already obtaining the PCA results,

you can definitely obtain the kinetic energies of the modes simply

with a couple of small calculations.

For more on PCA (Quasiharmonic Analysis) and deriving thermodynamic

relations from it, see Appendix C (pp 18-22) of:

http://oolung.chem.ku.edu/~kuczera/Public/web/html/lect/nma/nma.html.

Jeff

On Apr 8, 2009, at 8:59 PM, JT wrote:

*> 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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