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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