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

From: Chris Moth <>
Date: Wed, 02 Apr 2008 16:09:14 -0500

You might try the "analyze matrix" command in ptraj.

I see this around page 259 of the Amber9 manual:

"thermo" calculates entropy, heat capacity, and internal energy from the
structure of
a molecule (average coordinates, see above) and its vibrational
frequencies using
standard statistical mechanical formulas for an ideal gas. This option
is only available
for mwcovar matrices.

Add something like:

analyze matrix mwcvmat out filename thermo [vecs vecs] [reduce]

to what you have already done.

Seth Lilavivat wrote:
> 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/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.
> Thanks,
> Seth

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