From: JT (JTibbitt_at_odu.edu)
Date: Fri Apr 10 2009 - 11:36:52 CDT
I don't think I understand your problem. I thought you are trying to
find atomic velocites of atoms along single PCA modes, so that you
could calculate the kinetic energy of each mode. The method of PCA
incorporates anharmonicity by generating modes that match the
covariance matrix supplied from the MD run. But the resultant modes
produced are normal harmonic vibrations. And the velocities could be
obtained from them. But if you are doing something different, then I
Axel already supplied an excellent suggestion. Write out both
coordinate and velocity DCD trajectories (each every 100 steps). Then
just using the verlet scheme to generate the before and after
On Apr 10, 2009, at 11:14 AM, Mert Gür wrote:
> Dear Jeff,
> The link that you posted was quite helpfull. It is explaining the
> topic very clear. Really thank you for that.
> For MD, PCA simplifies to the NMA only in the limit of 0 degree
> when there is no unharmonicty present. The problem lies at this
> point if the motion where harmonic of course I would know its
> Kinetic energy with respect to time. This is so because velocity is
> defined for NMA as
> here w is frewuency and t is time.
> The probem is that;
> In unharmonic case I wont have this kind of relation. That is why I
> at least two need subsquent coordinates.
> Which brings me unfortunately back to my starting point.
> Dear Peter,
> As you said since I am doing modal decomposition first and then
> generate a DCD file for each mode by my own, I wont have the
> corresponding log file. I have to find somehow the velocities.
> On Thu, Apr 9, 2009 at 6:04 AM, JT <jtibbitt_at_odu.edu> wrote:
> 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
> 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
> For more on PCA (Quasiharmonic Analysis) and deriving thermodynamic
> relations from it, see Appendix C (pp 18-22) of:
> On Apr 8, 2009, at 8:59 PM, JT wrote:
>> 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.
>> 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.
>>> On Wed, Apr 8, 2009 at 11:15 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
>>> > wrote:
>>> Try writing a velocity DCD
>>> 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
>>> > and the kinetic energies of the selected modes.
>>> > If I am not mistaken , NAMD energy plugin gives me the potential
>>> > 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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