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Molecular dynamics
About: Molecular dynamics is a research topic. Over the lifetime, 22482 publications have been published within this topic receiving 800625 citations. The topic is also known as: molecular dynamics.
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TL;DR: In this article, a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules is presented, which is based on Hill's formal theory of physical clustering.
Abstract: We present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules. The method is based on Hill’s formal theory of physical clusters. In the method, a molecular dynamics calculation is used to calculate the average potential energy of a cluster of molecules as a function of temperature, and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature. The method is illustrated by calculations of the equilibrium constants for the formation of clusters of two to five water molecules that interact with each other by an intermolecular potential devised by Watts. The method is compared with other procedures for calculating the thermodynamic properties of clusters.
3,263 citations
TL;DR: In this paper, an approach for predicting charge distributions in molecules for use in molecular dynamics simulations is presented, where an atomic chemical potential is constructed by using these quantities plus shielded electrostatic interactions between all charges.
Abstract: We report here an approach for predicting charge distributions in molecules for use in molecular dynamics simulations. The input data are experimental atomic ionization potentials, electron affinities, and atomic radii. An atomic chemical potential is constructed by using these quantities plus shielded electrostatic interactions between all charges. Requiring equal chemical potentials leads to equilibrium charges that depend upon geometry. This charge equilibration (QEq) approach leads to charges in excellent agreement with experimental dipole moments and with the atomic charges obtained from the electrostatic potentials of accurate ab initio calculations. QEq can be used to predict charges for any polymer, ceramic, semiconductor, or biological system, allowing extension of molecular dynamics studies to broad classes of new systems. The charges depend upon environment and change during molecular dynamics calculations. We indicate how this approach can also be used to predict infrared intensities, dielectric constants, and other charge-related properties.
2,820 citations
TL;DR: In this paper, it was shown that different pair potentials lead to different crystal structures, with the use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell.
Abstract: With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
2,630 citations
01 Aug 1981
TL;DR: In this paper, the authors present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules based on Hill's formal theory of physical clustering, which is used to calculate the average potential energy of a cluster of molecules as a function of temperature and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature.
Abstract: : We present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules. The method is based on Hill's formal theory of physical clusters. In the method, a molecular dynamics calculation is used to calculate the average potential energy of a cluster of molecules as a function of temperature, and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature. The method is illustrated by calculations of the equilibrium constants for the formation of clusters of two to five water molecules that interact with each other by an intermolecular potential devised by Watts. The method is compared with other procedures for calculating the thermodynamic properties of clusters. (Author)
2,629 citations
Book•
01 Jan 1996
TL;DR: In this article, the authors introduce the concept of Computational Quantum Mechanics (CQM) and present four challenges in molecular modelling: Free Energies, Solvation, Reactions and Solid-State Defects.
Abstract: Preface. Symbols and physical constants. 1. Useful Concepts in Molecular Modelling. 2. An Introduction to Computational Quantum Mechanics. 3. Advanced AB Initio Methods, Density Functional Theory and Solid-State Quantum Mechanics. 4. Force Field Models: Molecular Mechanics. 5. Energy Minimisation and Related Methods for Exploring the Energy Surface. 6. Computer Simulation Methods. 7. Molecular Dynamics Simulation Methods. 8. Monte Carlo Simulation Methods. 9. Conformational Analysis. 10. Protein Structure Prediction, Sequence Analysis and Protein Folding. 11. Four Challenges in Molecular Modelling: Free Energies, Solvation, Reactions and Solid-State Defects. 12. The Use of Molecular Modelling and Chemoinformatics to Discover and Design New Molecules.
2,457 citations