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

The GPU Optimized Monte Carlo (GOMC) simulation engine is one of the fastest open-source Monte Carlo engines. Molecular Simulation Design Framework (MoSDeF) software is an open-source software package that efficiently constructs simple or complex chemical systems, applies the force field parameters, and writes several simulation input files. MoSDeF-GOMC uses the power of MoSDeF to build the traditional chemical engineering system, while MoSDeF-GOMC generates all the required files to perform a GOMC simulation.

The MoSDeF-GOMC software is compatible with the following software or simulation methods, when the files are generated with the Lennard-Jones (LJ) non-bonded potential:

1. The NAMD molecular dynamics software: The NAMD control file needs to be created by another means, but all the other files (PDB, PSF, and force field files) are compatible.

2. The py-MCMD software (Hybrid Monte Carlo and molecular dynamics simulations via GOMC and NAMD): All files are compatible except the GOMC control file (PDB, PSF, and force field files) are compatible.

3. Switching back and forth, in any order or duration, between a GOMC and NAMD simulations, allowing faster equilibrium for GOMC simulations and many other advantages. The newest GOMC versions also retain the atom/bead velocities and pass them back to NAMD.

MoSDeF-GOMC Highlights:

1. With tens of lines of MoSDeF-GOMC code, you can generate all the required files to conduct a GOMC simulation (see Simple MoSDeF-GOMC examples).

2. MoSDeF-GOMC is designed to automate the simulation workflow, allowing high-throughput workflows with GOMC or NAMD, where signac can be utilized to manage the simulations, data storage, and analysis.

3. MoSDeF-GOMC lowers the barrier of entry for novice users.

4. MoSDeF-GOMC and MoSDeF permit reproducible simulations, as these automated simulation workflows can build, simulate, and analyze the data in a repeatable manner. This allows the simulation workflows to be easily transferred, replicated, or expanded upon within or outside existing teams.

Overview

• General Information
  • MoSDeF-GOMC Basics
  • MoSDeF-GOMC is a part of the MoSDeF ecosystem
• Supported Chemical Systems
  • Traditional Chemical Engineering Systems
  • Non-Traditional Chemical Engineering Systems

Getting Started

• Installation
  • Install with mamba (Recommended)
  • Install with conda
  • Install an editable version from the source code
  • Install pre-commit
  • Supported Python Versions
  • Testing your installation
  • Building the documentation
• Quick Start
  • Build A System and Write All Files
  • Examples Repositories

Topic Guides

• Data Structures
  • CHARMM-style PDB, PSF, and Force Field File Writers
  • GOMC Control File Writer
  • NAMD Control File Writer
  • MoSDeF software functions
• Loading Data

Reference

• Units
• User Notices
• Credits
• Citing