Hi, 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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