Absolute entropies from molecular dynamics simulation trajectories

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Abstract
A heuristic formula for calculating absolute entropies from the covariance matrix of atom-positional fluctuations was extensively tested. Because of its heuristic nature, the results obtained are compared to analytical expressions for an ensemble of harmonic oscillators, for the ideal gas, and to numerical results obtained from the equation of state for the Lennard-Jones fluid as a means of validation of the approximate formula for the entropy. The formula yields rather accurate results. The removal of translational and rotational rigid body motion and the effect of the various fitting procedures involved are discussed for the more realistic system of a β-heptapeptide in solution.