AMBER: ptraj / covariance / quasiharmonic approximation / entropy

From: Seth Lilavivat <>
Date: Wed, 2 Apr 2008 15:18:55 -0400

Dear Amber users,

I am trying to use ptraj to calculate entropy from diagonalizing the
covariance matrix. I would also like to select subsets of atoms to
approximate entropy from this particular group of atoms (i.e. backbone of
DNA). I'm not sure if I am using ptraj correctly. This is what I have so

trajin ../output/prod1-5ns.dcd
matrix mwcovar name mwcvmat .P,O3',O5',C3',C4',C5'

Is this correct so far? If so how would I use the "analyze matrix" command
to now calculate entropy? Your help is always appreciated.


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Received on Fri Apr 18 2008 - 21:16:15 PDT
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