Exploring molecular dynamics with forces from n-body potentials using Matlab

TL;DR

This paper introduces MATLAB-based methods for simulating molecular dynamics with n-body potentials, focusing on educational and development purposes rather than large-scale applications, and explores three-body force calculations.

Contribution

It presents MATLAB and Octave implementations for n-body molecular dynamics simulations, emphasizing three-body interactions and providing accessible code for educational use.

Findings

Methods enable exploration of three-body forces in molecular dynamics.

MATLAB and Octave implementations are provided for educational purposes.

Framework can be extended to general n-body interactions.

Abstract

We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of the simulations, or simply for instruction and education purposes. We also present exploration of forces obtained from 3-body potentials in Molecular Dynamics in this framework. The methods are based on use of matrices and multidimensional arrays for which MATLAB has a set of both linear algebra based as well as element-wise operations. Applications to three-body interactions are the main aspect of this work, but extension to any general form of n-body interactions is also discussed. The methods discussed can be also applied without any change using the latest versions of the package GNU OCTAVE as a replacement for MATLAB. The code examples are listed in some detail, a full package of the MATLAB and OCTAVE codes is available for download.