[gmx-users] Normal Mode Analysis

[Tsjerk Wassenaar]

Hi James,

PCA on a trajectory is about fluctuations -the correlation between
deviations from an average positions-, NMA is about penalized
displacement -the increase in potential energy due to concurrent
displacement-. In NMA the lowest mode is that for which most atoms can
move most unrestrictedly. It seems evident that the side chains will
severely penalize the displacement of c-alpha atoms. I wouldn't call
that a solvent effect or damping. It's the nature of the protein, and
the error you make in your model when restricting to c-alpha atoms
only.

With respect to the other question, I think the best I can do is to
urge you to read more on principal component analysis, until you
understand the meaning of 'principal component', 'eigenvalue',
'score', 'projection' and 'loading' :)

Cheers,

Tsjerk

On Thu, Nov 10, 2011 at 8:51 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Hi Tsjerk,
>
> Thanks for help. So as I understood if I want to calculate fluctuations only
> for Calpha I must first to do NMA of my reference in some mode subspace
> consisted of the eigenvectors for Calpha atoms only. Does this correct ?
> Previously I've done something like this for random subspace of modes in
> MMTK (just to reduce the space for calculation) but how perform such
> operation in Gromacs I havent known yet :)
>
>
>> The c-alphas are less hindered in the second model due to the absence
>> of the side chains and such. There's just more freedom.
>>
>
> It's known that solevnt for instance could significant damp motions from
> normal modes. So in my case It seems that sidechains act as the solvent. How
> do you think may sidechains not only damp motions oberved for C-alpha atoms
> merely but also change the trajectory of their motion?
>
>
> James
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands