Interaction Models for Water in Relation to Protein Hydration

@inproceedings{Berendsen1981InteractionMF,
  title={Interaction Models for Water in Relation to Protein Hydration},
  author={Herman J. C. Berendsen and Johan P. M. Postma and Wilfred F. van Gunsteren and Jan Hermans},
  year={1981}
}
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… 

Figures and Tables from this paper

Molecular Dynamics Simulations of Proteins:  Can the Explicit Water Model Be Varied?
TLDR
The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.
Simple model of hydrophobic hydration.
TLDR
A 2-dimensional Mercedes-Benz-like model of water is developed with which the free energy, enthalpy, entropy, and the heat capacity of transfer as a function of temperature, pressure, and solute size is computed.
A polarizable water model for calculation of hydration energies
A molecular model for electronic polarization of water is defined, consisting of interacting point dipole polarizabilities in an electric field generated by atomic point charges, which represent the
Effects of ion–water Lennard-Jones potentials on the hydration dynamics around a monovalent atomic ion in molecular dynamics simulations
ABSTRACT The molecular dynamics (MD) method is a promising technique to dissect the atomistic details of water dynamics around a solute. However, the quantitative predictions of experimentally
Parameterization and evaluation of a flexible water model
  • D. Ferguson
  • Chemistry, Computer Science
    J. Comput. Chem.
  • 1995
TLDR
The results indicate that an increased Lennard‐Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ⃛ O radial distribution function of water at 298 K and 1 atm.
Simulations of Proteins in Water a
TLDR
A 40-psec simulation on crystalline PTI, involving 4 protein molecules (of 58 amino acids each), 552 water molecules, and 24 Cl- ions is described, to evaluate the accuracy and reliability of molecular dynamics simulations of hydrated proteins.
A molecular model of water based on the lattice gas model
A lattice gas model is used to describe the vapor-liquid state of water molecules. The orientationally directed interaction of the water molecules via their tetrahedral structure and dipole-dipole
Polarizable Water Potential Derived from a Model Electron Density.
TLDR
This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields.
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations
TLDR
Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined.
Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions
Abstract A new program package (COSMOS90) for molecular dynamics simulations was developed to simulate large molecular systems consisting of more than tens of thousands of atoms without the
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 23 REFERENCES
Improved simulation of liquid water by molecular dynamics
Molecular dynamics calculations on a classical model for liquid water have been carried out at mass density 1 g/cm3 and at four temperatures. The effective pair potential employed is based on a
Molecular Dynamics Study of Liquid Water
A sample of water, consisting of 216 rigid molecules at mass density 1 gm/cm3, has been simulated by computer using the molecular dynamics technique. The system evolves in time by the laws of
Study of the structure of molecular complexes. XIII. Monte Carlo simulation of liquid water with a configuration interaction pair potential
A water–water interaction potential obtained from configuration interaction calculations has been used to simulate liquid water, at 25 °C, by a Monte Carlo technique. The resulting radial
Picosecond dynamics of tyrosine side chains in proteins.
TLDR
A dynamical analysis of the orientation fluctuations of two tyrosine side chains in the bovine pancreatic trypsin inhibitor is presented and it is found that the Langevin equation is applicable to the ring torsional motion, which corresponds to that of an angular harmonic oscillator with near-critical damping.
ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS
The application of the computer simulation method of molecular dynamics to macromolecules is investigated. The protein trypsin inhibitor (BPTI), consisting of 454 united atoms, is used as an example.
CI study of the water dimer potential surface
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
Convergence characteristics of Monte Carlo–Metropolis computer simulations on liquid water
Very long (∼5000 K) Monte Carlo computer simulations are reported for liquid water described in terms of the analytical potential functions of Matsuoka, Clementi, and Yoshimine and Rahman and
Protein structural fluctuations during a period of 100 ps
TLDR
Analysis of the present simulation of PTI has confirmed most of the conclusions of the earlier study but has shown that there are significant features of the dynamics that can be observed only over a longer period, ∼100 ps.
Cooperative effects in simulated water
Computer simulation calculations on liquid water, aqueous solutions and biological interfaces have been made almost universally assuming pair-additive interactions. Experimental and theoretical
Dynamics of folded proteins
TLDR
The dynamics of a folded globular protein have been studied by solving the equations of motion for the atoms with an empirical potential energy function and suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.
...
1
2
3
...