calcraven / mosdef-gomc

MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC

MoSDeF-GOMC:

A User-Friendly Python Interface for Creating All of the files required to run a GPU Optimized Monte Carlo (GOMC) simulation engine via the Molecular Simulation Design Framework Molecular Simulation Design Framework (MoSDeF) (MoSDeF Github) software.

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Overview

This Python code allows the auto-generation of the GPU Optimized Monte Carlo (GOMC) files for a simulation, which includes the coordinate (PDB), topology (PSF), force field (FF), and the GOMC control file. This software supports various systems, force field types, and can also create the PDB, PSF, and FF files for the NAMD simulation engine. Since MoSDeF-GOMC was built from the Molecular Simulation Design Framework (MoSDeF) (MoSDeF Github) platform, it provides complete integration with the MoSDeF software.

Warning

MoSDeF-GOMC is a new product continually adding functionality to provide an optimal user experience. Therefore, there could be some user-noticeable changes to this software when upgrading newer MoSDeF-GOMC versions.

The original version of MoSDeF-GOMC, which uses Parmed as the software backend, will be deprecated by December 2022. This Parmed version is already replaced with the new MoSDeF-GOMC version, which uses MoSDeF's GMSO software as the new backend. We recommend that the new GMSO version of MoSDeF-GOMC be used because it has many new features, and the Parmed is no longer supported.

Resources

• GOMC Github repository
• Downloading GOMC
• Installing GOMC via GOMC manual
• MoSDeF-GOMC tutorials and examples with MoSDeF-GOMC YouTube videos
• GOMC YouTube channel
• MoSDeF tools

Citation

Please cite MoSDeF-GOMC, GOMC, and MoSDeF tools, which are provided here.

Documentation

The MoSDeF-GOMC documentation is located here.

Installation

The recommended MoSDeF-GOMC package installation is with mamba:

conda create --name mosdef_gomc python=3.10

conda activate mosdef_gomc

conda install -c conda-forge mamba

mamba install -c conda-forge mosdef-gomc

The MoSDeF-GOMC package is also available via conda, but conda has had some issues pulling the most recent packages (user beware):

conda create --name mosdef_gomc -c conda-forge mosdef-gomc python=3.10

NOTE: conda has had some issues pulling the most recent packages, so a mamba installation is recommended.