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The Molecular Dynamics Method: An Introduction
2016An introduction to modern molecular dynamics computer simulations of organic functional materials and to applications in organic electronics, particularly ...
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1993
This Chapter describes the basic molecular dynamics method for simulating atoms in the microcanonical ensemble. The extension of the technique for studying molecules of arbitrary complexity using constraint dynamics is outlined and three algorithms for solving the equations of motion of the constraints are discussed.
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This Chapter describes the basic molecular dynamics method for simulating atoms in the microcanonical ensemble. The extension of the technique for studying molecules of arbitrary complexity using constraint dynamics is outlined and three algorithms for solving the equations of motion of the constraints are discussed.
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An optimized replica exchange molecular dynamics method
The Journal of Chemical Physics, 2009We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved.
Hiqmet, Kamberaj, Arjan, van der Vaart
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Canonical numerical methods for molecular dynamics simulations
Journal of Computational Chemistry, 1994AbstractWe consider the application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard–Jones interaction ...
Daniel I. Okunbor, Robert D. Skeel
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1990
Although macromolecules have been traditionally described in terms of rigid and unique three-dimensional structures, the dynamics of these molecules have become increasingly important in the understanding the relationships between structure and mechanism.
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Although macromolecules have been traditionally described in terms of rigid and unique three-dimensional structures, the dynamics of these molecules have become increasingly important in the understanding the relationships between structure and mechanism.
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Direct anharmonic correction method by molecular dynamics
Computer Physics Communications, 2017Abstract The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties , the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI)
Zhong-Li Liu +4 more
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Integration Methods for Molecular Dynamics
1996Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor ...
Benedict J. Leimkuhler +2 more
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Molecular dynamic simulation methods for anisotropic liquids
The Journal of Chemical Physics, 2004Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially
Keiko M, Aoki +2 more
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New Molecular-Dynamics Method for Metallic Systems
Physical Review Letters, 1985We present a new formulation for simulations of metallic systems which allows for volume and shape variations and incorporates explicitly the dependence on density of the ''volume energy'' and the effective pair potentials. Simulations of liquid Mg yield good agreement with experiments for several properties including internal energy, density, and ...
, Barnett, , Cleveland, , Landman
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Reweighting methods for Molecular Dynamics
2019The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems.
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