Hi all<br><br>I have a query about the eigenvalue values obtained from g_covar and g_anaeig<br><br>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 <br>
<br> 1 10.1064<br> 2 4.78616<br> 3 4.07406<br> 4 3.48535<br> 5 2.7176<br> 6 2.13348<br> 7 1.75909<br> 8 1.45699<br> 9 1.12932<br> 10 0.893933<br>
<br>What i infer from this is that the cumulative variance experienced by the top 10 PC is hardly ~ 30 %. <br><br>so my questions are<br><br>a) does this imply inadequate sampling by MD or a limited conformational change happening in the system???? <br>
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.<br><br>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.<br>
<br>Regards<br>Vijayan.R<br>