P.O. Fedichev, E.G. Getmantsev, L.I. Men’shikov
(Submitted on 12 Aug 2009 (v1), last revised 9 Dec 2009 (this version, v2))
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.
Comments: 6 pages, 4 figures, more results, examples and references added
Subjects: Quantitative Methods (q-bio.QM); Chemical Physics (physics.chem-ph)
Cite as: arXiv:0908.1708v2 [q-bio.QM]

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