AMBER Archive (2008)

Subject: AMBER: ptraj / covariance / quasiharmonic approximation / entropy

From: Seth Lilavivat (
Date: Wed Apr 02 2008 - 14:18:55 CDT

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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