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

[R.S.K.Vijayan]

Hi all

I have a query about  the eigenvalue values obtained from g_covar and
g_anaeig

I performed essential dynamics using  PCA on my system (Protein-DNA
complex) considering BB of the protein and the phosphate and sugar of the
DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10
principal components are stated below

         1 10.1064
         2 4.78616
         3 4.07406
         4 3.48535
         5 2.7176
         6 2.13348
         7 1.75909
         8 1.45699
         9 1.12932
        10 0.893933

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

so my questions are

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

Thanking you in advance for your suggestions. My apologies since it sound
to be a very general question and rather not very specific to Gromacs.

Regards
Vijayan.R
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