MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

Crawford, Brad; Timalsina, Umesh; Quach, Co D.; Craven, Nicholas C.; Gilmer, Justin; McCabe, Clare; Cummings, Peter T.; Potoff, Jeffrey J.

doi:10.1021/acs.jcim.2c01498

J. Chem. Inf. Model.

2023

DOI: 10.1021/acs.jcim.2c01498

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MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

Brad Crawford

Umesh Timalsina

Co D. Quach

et al.

Abstract: 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… Show more

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Cited by 3 publications

References 120 publications

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Comparison of 3D-cDFT and GCMC simulations for fluid–structure analysis in amorphous carbon nanoporous materials

Santos,

Soares,

Barreto

et al. 2024

Adsorption

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Investigating fluid behavior in nanoporous materials is essential for gas storage, separation, and catalysis applications. Here, we present a comparison of two computational methods for fluid-structure analysis in amorphous nanoporous carbon materials: three-dimensional (3D) classical Density Functional Theory (cDFT) and Grand Canonical Monte Carlo (GCMC) simulations. We extended our recent development of 3D-cDFT to allow density-profile analysis without symmetry assumptions, enhancing its applicability to a broader range of porous materials. We provide a theoretical overview and discuss the advantages and limitations of each method. Our results highlight the accuracy of both 3D-cDFT and GCMC simulations while emphasizing differences in computational cost, precision, and scope. We also explore the impact of the non-crystalline structure of amorphous carbon nanopores on fluid structure and adsorption isotherms, as well as fluid-fluid and fluid-solid interactions. We offer insights for selecting computational methods in fluid structure analysis of nanoporous materials, guiding future research and optimization in advanced material development for diverse applications.

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Comparison of 3D-cDFT and GCMC simulations for fluid–structure analysis in amorphous carbon nanoporous materials

Santos,

Soares,

Barreto

et al. 2024

Adsorption

View full text Add to dashboard Cite

show abstract

MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

Crawford

Timalsina

Quach

et al. 2023

J. Chem. Inf. Model.

Self Cite

View full text Add to dashboard Cite

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 .

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pyMBE: The Python-based molecule builder for ESPResSo

Beyer,

Torres,

Pineda

et al. 2024

The Journal of Chemical Physics

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We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides, and globular proteins in the Extensible Simulation Package for Research on Soft Matter (ESPResSo). The Python interface of ESPResSo offers a flexible framework, capable of building custom CG models from scratch. As a downside, building CG models from scratch is prone to mistakes, especially for newcomers in the field of CG modeling, or for molecules with complex architectures. The pyMBE module builds CG models in ESPResSo using a hierarchical bottom-up approach, providing a robust tool to automate the setup of CG models and helping new users prevent common mistakes. ESPResSo features the constant pH (cpH) and grand-reaction (G-RxMC) methods, which have been designed to study chemical reaction equilibria in macromolecular systems with many reactive species. However, setting up these methods for systems, which contain several types of reactive groups, is an error-prone task, especially for beginners. The pyMBE module enables the automatic setup of cpH and G-RxMC simulations in ESPResSo, lowering the barrier for newcomers and opening the door to investigate complex systems not studied with these methods yet. To demonstrate some of the applications of pyMBE, we showcase several case studies where we successfully reproduce previously published simulations of charge-regulating peptides and globular proteins in bulk solution and weak polyelectrolytes in dialysis. The pyMBE module is publicly available as a GitHub repository (https://github.com/pyMBE-dev/pyMBE), which includes its source code and various sample and test scripts, including the ones that we used to generate the data presented in this article.

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MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

Cited by 3 publications

References 120 publications

Comparison of 3D-cDFT and GCMC simulations for fluid–structure analysis in amorphous carbon nanoporous materials

Comparison of 3D-cDFT and GCMC simulations for fluid–structure analysis in amorphous carbon nanoporous materials

MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC

pyMBE: The Python-based molecule builder for ESPResSo

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