Molecular Dynamics Simulations

TL;DR

This paper provides a comprehensive tutorial on Molecular Dynamics simulations, covering algorithms, ensembles, and applications like molten SiO2 and polymer melts under shear, highlighting their scope and practical results.

Contribution

It offers an introductory overview of MD techniques, algorithms, and applications, connecting them to other simulation methods and illustrating with specific examples.

Findings

Estimation of transport coefficients for molten SiO2

Simulation of polymer melt under shear

Discussion of sampling in different ensembles

Abstract

A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is discussed. As an example of Non-Equilibrium Molecular Dynamics (NEMD), a study of a glass-forming polymer melt under shear is mentioned.