AMBER Archive (2008)Subject: AMBER: ptraj / covariance / quasiharmonic approximation / entropy
From: Seth Lilavivat (sethl_at_gatech.edu)
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
far:
trajin ../output/prod15ns.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.
Thanks,
Seth

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