O(N) continuous electrostatics solvation energies calculation method for biomolecules simulations

Details O(N) continuous electrostatics solvation energies calculation method for biomolecules simulations O(N) continuous electrostatics solvation energies calculation method for biomolecules simulations

2009-08-12

arxiv.org/abs/0908.1708v2

J Comput Chem. 52, 1368-76, 2011

Biology

Quantitative Biology

Quantitative Methods

6 pages, 4 figures, more results, examples and references added

Scientific paper

10.1002/jcc.21719

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory requirements, is only a few percent wrong for any molecular configurations of arbitrary sizes, gives explicit value for the reaction field potential at any point, provides both the solvation energy and its derivatives suitable for Molecular Dynamics simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies of molecular complex formation.

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