[gmx-users] entropy calculation

soumadwip ghosh soumadwipghosh at gmail.com
Sat Apr 11 07:32:51 CEST 2015

    You did not mention what kind of system you are dealing with nor the
type of entropy you want to calculate. If you want to calculate the entropy
of binding (say protein and a nucleic acid) you should calculate PMF by any
method at different temperature and the decomposition of the temperature
dependent free energies will give you entropy (of binding!!). Otherwise, if
you want to calculate the configurational entropy of a system or a part of
it, you should use g_covar in conjugation with g_anaeig. The first command
will perform a covariance analysis of the coordinates of the system and
prodeuce eigenvalues which has now to be analyzed by g_anaeig. With
-entropy flag you will get the configurational entropies by two methods at
a certain temperature.


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