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A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations

✍ Scribed by Luis Lorenzo; Ricardo A. Mosquera

Publisher
John Wiley and Sons
Year
2003
Tongue
English
Weight
97 KB
Volume
24
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

A box‐counting‐based algorithm (SEBC) has been developed for the numerical computation of the Shannon entropy from samples of continuous functions. Its performance was tested by applying it to several samples of known continuous distribution functions. The results obtained with SEBC reproduced those obtained by analytical or numerical integration. SEBC was also employed for computing the Shannon entropies of the steric energy, Sh(E~S~), of several amino acids from their in vacuo NVE molecular dynamics simulations using the AMBER‐4 force field. The results obtained correlate linearly with the experimental standard thermodynamic entropies of these compounds. This work points to the possibility of introducing straightforward and reliable calculations of thermodynamic entropies from empirical linear relationships with Sh(E~S~) obtained from MD simulations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 707–713, 2003

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