Premium
Numerical interpretation of molecular surface field in dielectric modeling of solvation
Author(s) -
Wang Changhao,
Xiao Li,
Luo Ray
Publication year - 2017
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.24782
Subject(s) - molecular dynamics , dielectric , statistical physics , force field (fiction) , solvation , boundary value problem , field (mathematics) , representation (politics) , surface (topology) , computer science , computational chemistry , computational physics , physics , mathematics , chemistry , mathematical analysis , molecule , quantum mechanics , geometry , politics , political science , pure mathematics , law
Continuum solvent models, particularly those based on the Poisson‐Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one‐sided and two‐sided methods with both first‐order and second‐order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one‐dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface‐to‐atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second‐order methods, including the one‐dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one‐dimensional method is far more efficient than standard second‐order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc.