Higher-order symplectic integration techniques for molecular dynamics problems

AbstractWe will present a general formalism for deriving boundary conditions for molecular dynamics simulations of crystalline solids in the context of atomistic/continuum coupling. These boundary conditions are modeled by generalized Langevin equations, derived from Mori-Zwanzig's formalism. Such boundary conditions are useful in suppressing phonon reflections, and maintaining the system temperature.

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Molecular dynamics and higher-order perturbation-theory results for the anharmonic free energy and equation of state of a Lennard-Jones solid

Physical Review B ◽

10.1103/physrevb.54.3266 ◽

1996 ◽

Vol 54 (5) ◽

pp. 3266-3272 ◽

Cited By ~ 17

Author(s):

Daniel J. Lacks ◽

Ramesh C. Shukla

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Theory ◽

Equation Of State ◽

Higher Order ◽

Order Perturbation ◽

Order Perturbation Theory ◽

Lennard Jones

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Packing Density Insensitive Contact Detection Algorithm for Molecular Dynamics Simulations

Volume 2: Automotive Systems; Bioengineering and Biomedical Technology; Computational Mechanics; Controls; Dynamical Systems ◽

10.1115/esda2008-59100 ◽

2008 ◽

Author(s):

A. Munjiza

Keyword(s):

Molecular Dynamics ◽

Packing Density ◽

Detection Algorithm ◽

Contact Detection ◽

Dense Gases ◽

Large Numbers ◽

Dynamics Simulations ◽

Interacting Atoms ◽

Dynamics Problems ◽

Contact Detection Algorithm

Molecular dynamics problems involve large numbers of interacting atoms requiring CPU and RAM intensive computational simulations. A contact detection algorithm which detects pairs of interacting atoms is a key component of these simulations. This paper presents a contact detection algorithm that is completely insensitive to packing density in terms of both RAM and CPU requirements — thus permitting near vacuum conditions and dense gases or liquids to coexist in the same simulation. In addition, both CPU and RAM requirements are proportional to the total number of atoms.

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Usage of graphics processing units for solving molecular dynamics problems

Proceedings of the Mavlyutov Institute of Mechanics ◽

10.21662/uim2011.1.017 ◽

2011 ◽

Vol 8 (1) ◽

pp. 182-188

Author(s):

D.F. Marin

Keyword(s):

Molecular Dynamics ◽

Graphics Processing Units ◽

Computational Scheme ◽

Lennard Jones Potential ◽

Jones Potential ◽

Lennard Jones ◽

Graphics Processing ◽

Dynamics Problems

The paper presents results on performance and efficiency of GPU utilization in a simulation of molecular dynamics processes. The simulation was done with the usage of Lennard-Jones potential and leapfrog computational scheme.

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