Argon Simulations with EM3, a New Modular Molecular Mechanics Program

TL;DR

This paper introduces EM3, a modular, object-oriented molecular mechanics program for argon simulations, validated against Monte Carlo results and demonstrating extendibility and educational value.

Contribution

The paper presents EM3, a new open-source, modular molecular mechanics program designed with object-oriented principles for argon simulations and educational use.

Findings

EM3 accurately reproduces Monte Carlo results for argon.

The program successfully calculates the self-diffusion coefficient.

EM3 demonstrates extendibility and modularity for molecular simulations.

Abstract

Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of a functioning MD program. An organizational scheme for a general molecular mechanics program is therefore presented, along with the framework of the EM3 program. With the modular nature and open-source availability, EM3 can serve as a learning tool for newcomers to molecular simulations and code organization via object-oriented programming. Validations of the code are presented in comparison with Monte Carlo (MC) simulations of liquid argon at different densities and temperatures. A calculation of the self-diffusion coefficient for liquid argon is also performed, exhibiting the extendibility of EM3. This report comes packaged with the EM3 source code and examples, located at https://github.com/rohskopf/em3.