TY - JOUR
T1 - MoSDeF-GOMC
T2 - Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC
AU - Crawford, Brad
AU - Timalsina, Umesh
AU - Quach, Co D.
AU - Craven, Nicholas C.
AU - Gilmer, Justin B.
AU - McCabe, Clare
AU - Cummings, Peter T.
AU - Potoff, Jeffrey J.
N1 - Funding Information:
This research was partially supported by the National Science Foundation (grants OAC-1835713, OAC-1835874 and CBET 2052438). Some of the computational resources used in this work were provided by the Wayne State University Grid computing environment.
Publisher Copyright:
© 2023 American Chemical Society.
PY - 2023/2/27
Y1 - 2023/2/27
N2 - MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC’s capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.
AB - MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC’s capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.
UR - http://www.scopus.com/inward/record.url?scp=85148963560&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.2c01498
DO - 10.1021/acs.jcim.2c01498
M3 - Article
C2 - 36791286
AN - SCOPUS:85148963560
SN - 1549-9596
VL - 63
SP - 1218
EP - 1228
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 4
ER -