Journal ArticleDOI
On the force bias Monte Carlo simulation of water: methodology, optimization and comparison with molecular dynamics
M. Rao,C. Pangali,Bruce J. Berne +2 more
TLDR
In this paper, an optimized version of the force bias scheme is presented for the Monte Carlo simulation of water in which the random walk of the individual molecule is biased in the direction of the forces and torque acting on the molecule.Abstract:
An optimized version of the force bias scheme is presented for the Monte Carlo simulation of water in which the random walk of the individual molecule is biased in the direction of the force and torque acting on the molecule. A new criterion is developed to judge the efficiency of sampling the configuration space by studying the translational and rotational diffusion of individual molecules during the random walk. The force bias method is compared with the uniform sampling method using ST2 water as an example, and with molecular dynamics. Similarities and differences between molecular dynamics and Monte Carlo are discussed with respect to pair correlations and energy distributions.read more
Citations
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Probabilistic Inference Using Markov Chain Monte Carlo Methods
TL;DR: The role of probabilistic inference in artificial intelligence is outlined, the theory of Markov chains is presented, and various Markov chain Monte Carlo algorithms are described, along with a number of supporting techniques.
Journal ArticleDOI
Calculations of electrostatic interactions in biological systems and in solutions.
Arieh Warshel,S.T. Russell +1 more
TL;DR: The key requirement for quantative understanding of the action of biological molecules is the ability to correlate electrostatic interactions with structural information, and the electrostatic free energy can be approximated by the Born formula.
Journal ArticleDOI
Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
TL;DR: In this paper, path integral molecular dynamics (PIMD) and path integral hybrid Monte Carlo (PIHMC) algorithms were developed for electron solvation in fluid helium and xenon.
Journal ArticleDOI
A Monte Carlo simulation of the hydrophobic interaction
C. Pangali,M. Rao,Bruce J. Berne +2 more
TL;DR: In this paper, the hydrophobic interaction between two apolar (Lennard-Jones) spheres dissolved in a model of liquid water (ST 2 water) is simulated using the force-bias Monte Carlo technique.
Journal ArticleDOI
A quantum mechanical study of structure in liquid H2O and D2O
TL;DR: In this article, path integral Monte Carlo methods are applied to the ST2 model of water to examine both the importance of quantum effects on the structure of liquid water and the differences in the structures of light and heavy water.
References
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Journal ArticleDOI
Equation of state calculations by fast computing machines
TL;DR: In this article, a modified Monte Carlo integration over configuration space is used to investigate the properties of a two-dimensional rigid-sphere system with a set of interacting individual molecules, and the results are compared to free volume equations of state and a four-term virial coefficient expansion.
Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Journal ArticleDOI
Improved simulation of liquid water by molecular dynamics
TL;DR: In this paper, a four-charge model for each molecule and a modification of the prior ''BNS'' interaction was proposed to improve the fidelity of the molecular dynamics simulation, leading to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x-ray scattering experiments.
Journal ArticleDOI
Molecular Dynamics Study of Liquid Water
TL;DR: In this paper, 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, subject to an effective pair potential that incorporates the principal structural effects of manybody interactions in real water.
Journal ArticleDOI
Monte Carlo studies of the dielectric properties of water-like models
J.A. Barker,R.O. Watts +1 more
TL;DR: In this article, Monte Carlo studies of the dielectric properties of water-like models were performed in order to understand the properties of the water-based models in terms of their dielectrics.