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Effective water model for Monte Carlo simulations of proteins
Author(s) -
Banks Jay,
Brower Richard C.,
Ma Jianpeng
Publication year - 1995
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360350308
Subject(s) - solvation , monte carlo method , statistical physics , molecular dynamics , dielectric , implicit solvation , chemistry , water model , quantum monte carlo , dynamic monte carlo method , physics , molecule , computational chemistry , quantum mechanics , statistics , mathematics , organic chemistry
We present an effective theory for water. Our goal is to formulate on accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all‐atom potential with a local dielectric density field, with self interactions given by the Landau‐Ginzburg free energy and external interactions by Lennard‐Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data‐parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvalion energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the non electrostatic contributions with estimates of hydrophohic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations, We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydroxen‐bonding terms. © 1995 John Wiley & Sons, Inc.