Title: Integrating Open Source Software Applications for Building Molecular Dynamics Systems
Presenter: Bruce Allen
Affiliation: University of Denver
Abstract: Open source software is used in the field of molecular dynamics. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and Virtual Molecular Dynamics software are two examples. Three open source applications, NanoEngineer-1, Packmol and mis2lmp are integrated using an open source file format to quickly create initial MD cells for molecular dynamics simulations. These three software applications collectively make up the open source software suite now known as Molecular Dynamics Studio (MDS). The software is validated through software engineering practices and through simulation of the Diglycidyl Ether of Bisphenol-A and Isophorone diamine (DGEBA-IPD) system to calculate, density, and glass transition temperature. Simulation results compare well with published experimental and simulation results.