AMBER Archive (2006)

Subject: AMBER: Entropy calculations with Nmode and ptraj

From: Daniel Oehme (oehmes4_at_gmail.com)
Date: Tue Apr 04 2006 - 02:24:39 CDT

Hi,

Our research group is investigating binding energy calculations and
are starting to do some entropy calculations. We have been able to do
these calculations using the mm_pbsa nmode script and also using ptraj
and the following commands:

trajin mtx_gas_solv_dynprod.mdcrd
strip :WAT
image
rms first *
matrix mwcovar name mwcvmat
analyze matrix mwcvmat thermo reduce
go

We dont have much background in doing entropy calculations and were
wondering if there was any literature out there that we could read
that could help us get an understanding of these entropy calculation
methods.

Daniel Oehme
PhD Student,
La Trobe University
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