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Derivatives of molecular surface area and volume: Simple and exact analytical formulas
Author(s) -
Klenin Konstantin V.,
Tristram Frank,
Strunk Timo,
Wenzel Wolfgang
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21844
Subject(s) - simple (philosophy) , volume (thermodynamics) , surface (topology) , statistical physics , mathematics , computational chemistry , calculus (dental) , geometry , thermodynamics , chemistry , physics , philosophy , epistemology , medicine , dentistry
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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011