Journal ArticleDOI
Molecular Dynamics Study of Liquid Water
TLDR
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.Abstract:
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 classical dynamics, subject to an effective pair potential that incorporates the principal structural effects of many‐body interactions in real water. Both static structural properties and the kinetic behavior have been examined in considerable detail for a dynamics ``run'' at nominal temperature 34.3°C. In those few cases where direct comparisons with experiment can be made, agreement is moderately good; a simple energy rescaling of the potential (using the factor 1.06) however improves the closeness of agreement considerably. A sequence of stereoscopic pictures of the system's intermediate configurations reinforces conclusions inferred from the various ``run'' averages: (a) The liquid structure consists of a highly strained random hydrogen‐bond network which bears little structural resemblance to known aqueous crys...read more
Citations
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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
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.
Book ChapterDOI
Interaction Models for Water in Relation to Protein Hydration
TL;DR: In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.
Journal ArticleDOI
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
TL;DR: In this paper, an algorithm, called RATTLE, for integrating the equations of motion in molecular dynamics calculations for molecular models with internal constraints is presented. But it is based on the Verlet algorithm and retains the simplicity of using Cartesian coordinates for each of the atoms to describe the configuration of a molecule with internal constraint.
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
Dispersion and Absorption in Dielectrics I. Alternating Current Characteristics
Kenneth S. Cole,Robert H. Cole +1 more
TL;DR: In this paper, the locus of the dielectric constant in the complex plane was defined to be a circular arc with end points on the axis of reals and center below this axis.
Journal ArticleDOI
Relaxation Effects in Nuclear Magnetic Resonance Absorption
TL;DR: In this article, the authors studied the effect of the thermal motion of the magnetic nuclei upon the spin-spin interaction in a rigid lattice and the line width of the absorption line.