New Open Source Software for Building Molecular Dynamics Systems
Bruce M. Allen · Digital Commons - DU (University of Denver) · 2012
The context of this work is the development of open source software to support researchers to quickly build systems of molecules for molecular dynamics (MD) simulations. The goal is achieved through the integration of three open source programs by judicious modifications and creation of new source code, which allows the creation of molecular models, MD cells and the LAMMPS geometry input files. The software changes work together supporting an easy and intuitive process for simulation system creation. Creation of multiple MD cells for research simulations becomes quicker and provides needed standardization to the simulation process. The researcher can select from atomistic force fields or modify the software to use other force fields. The software has been validated by generating the glass transition temperature (Tg) and the bulk modulus for a cross-linked epoxy system composed of Diglycidyl Ether of Bisphenol-A and Isophorone diamine (DGEBA/IPD). The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) software is used to conduct the molecule dynamics simulations.