Integrating open-source software applications to build molecular dynamics systems.
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.
University of Denver, Daniel Felix Richie School of Engineering & Computer Science, Mechanical & Materials Engineering, 2390 South York Street, Denver, Colorado, 80210.
Bruce M
BM
Allen
Paul K
PK
Predecki
Maciej
M
Kumosa
large-scale atomic/molecular massively parallel simulator; molecular dynamics; open source; software integration