[gmx-users] Eigenvalue values from PCA (a general question)

[Tsjerk Wassenaar]

Hi Vijayan R.,

> What i infer from this is that the cumulative variance experienced by  the
> top 10 PC is  hardly ~ 30 %.

Not experienced...; It's the variance captured by the first ten PC's.

> a) does this imply inadequate sampling by MD or a limited conformational
> change happening  in the system????

No, not at all. It shows that the motions in your system can not be
adequately captured by linear combinations of atom fluctuations. The
system may be too flexible and/or there may be a lot of rotational
motion.

> b) is it wise to consider the Nucleic acid during essential dynamics or
> should it be discared and only the Protein BB or CA be considered.

Analysis with and without nucleic acids are just two different things.

Cheers,

Tsjerk

-- 
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