Integrating Open-Source Software Applications to Build Molecular Dynamics Systems

BM Allen and PK Predecki and M Kumosa, JOURNAL OF COMPUTATIONAL CHEMISTRY, 35, 756-764 (2014).

DOI: 10.1002/jcc.23537

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. (c) 2014 Wiley Periodicals, Inc.

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