For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.

Interaction Models for Water in Relation to Protein Hydration

Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant difference...

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package

Publisher Summary The chapter focuses on a general description of the force fields that are most commonly used at present, and it gives an indication of the directions of current research that may yield better functions in the near future. After a brief survey of current models, mostly generated during the 1990s, the focus of the chapter is on the general directions the field is taking in developing new models. The most commonly used protein force fields incorporate a relatively simple potential energy function: The emphasis is on the use of continuum methods to model the electrostatic effects of hydration and the introduction of polarizability to model the electronic response to changes in the environment. Some of the history and performance of widely used protein force fields based on an equation on simplest potential energy function or closely related equations are reviewed. The chapter outlines some promising developments that go beyond this, primarily by altering the way electrostatic interactions are treated. The use of atomic multipoles and off-center charge distributions, as well as attempts to incorporate electronic polarizability, are also discussed in the chapter.

https://dasher.wustl.edu/ponder/papers/advprotchem-66-27-03.pdf

Force fields for protein simulations

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

https://www.pnas.org/content/pnas/102/19/6665.full.pdf

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

The potential energies for the water dimer in various geometrical configurations have been calculated with a configuration–interaction method. The computed dimerization binding energies corresponding to the potential minima for the linear, cyclic, and bifurcated configurations are −5.6, −4.9, and −4.2 kcal/mol, respectively; the correlation effects account for −1.1, −1.2, and −0.9 kcal/mol, respectively, of the total binding energy for these three dimeric forms. The correlation effects for the entire potential surface have been analyzed in terms of inter‐ and intramolecular effects; the substantial coupling found between these effects, particularly in the vicinity of equilibrium position, is discussed. The computational technique employed, in particular an analysis on the selection criteria for the configuration state functions, is discussed, and its reliability is assessed. Two analytical expressions for the water dimer potential surface obtained by fitting the calculated energies are presented. The potential surface given here is being used to determine the structure of liquid water (in the pairwise approximation and with Monte Carlo techniques); this latter work will be reported elsewhere.

M. Yoshimine

Papers

CI study of the water dimer potential surface