AMBER Archive (2008)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Wed Apr 02 2008 - 16:09:14 CDT

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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