Hello Everyone, this is my first question.
I am trying to do a covariance analysis to find the significant degrees of
freedom in my protein. I have used CPPTRAJ to generate a covariance matrix
between all alpha-carbons in my protein chain, and I diagonalized the
matrix. My understanding of analyzing this matrix is that the largest
eigenvalues are your most significant degrees of freedom, which is simple
enough. The only issue is that the eigenvalues are perfectly sorted, which
doesn't make much sense to me. This would imply that the majority of
fluctuation in my protein happens at one end, while little to no
fluctuation happens in the rest of the protein.
Can someone please help me physically interpret this covariance matrix in
terms of which degrees of freedom are most significant in my protein?
Thank you
Joel
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Received on Sat Feb 20 2016 - 15:30:03 PST
