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Derivatives of molecular surface area and volume: Simple and exact analytical formulas

✍ Scribed by Konstantin V. Klenin; Frank Tristram; Timo Strunk; Wolfgang Wenzel

Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
519 KB
Volume
32
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy‐to‐use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear‐scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header‐only template library. Β© 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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