General Information
MoSDeF-GOMC Basics
The Molecular Simulation Design Framework (MoSDeF) software is the base software for MoSDeF-GOMC, which builds and force fields the systems inside the MoSDeF-GOMC. This MoSDeF-GOMC software generates the required files for simulating a system using the GPU Optimized Monte Carlo (GOMC) or the NAMD molecular dynamics software. The MoSDeF-GOMC software builds all the required files (PDB, PSF, force field, and GOMC control files) to conduct 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:
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.
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.
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.
The MoSDeF-GOMC software creates all these files using only tens of lines of Python code. The MoSDeF-GOMC and MoSDeF tools permit simulation reproducibility across a variety of simulation engines, removing the requirement of expert knowledge in all the engines to repeat, continue, or advance the existing research. Additionally, the MoSDeF-GOMC and MoSDeF software permits the auto-generation of numerous and distinct systems, allowing large-scale screening of materials and chemicals via signac to manage the simulations and data.
Note
The using MoSDeF-GOMC software to setup the GOMC and NAMD simulations, is made even easier via the MoSDeF-GOMC Examples and the GOMC Documentation, which contains links to the GOMC Manual, with GOMC YouTube tutorial videos. For the Lennard-Jones (LJ) non-bonded interactions, the MoSDeF-GOMC’s PDB, PSF, and force field files are identical to the NAMD files for the traditional chemical engineering simulations, unless there are fixed bonds and angles in the GOMC force field files. Changing the fixed bonds and angles between the GOMC and NAMD force field files is as simple as changing one (1) variable and rerunning that line of code, making a separate GOMC and NAMD files for the same system. Making separate files may be needed when running a hybrid Monte Carlo and molecular dynamics (GOMC and NAMD) simulation with the py-MCMD software .
MoSDeF-GOMC is a part of the MoSDeF ecosystem
The MoSDeF-GOMC software is a liaison between the Molecular Simulation Design Framework (MoSDeF) software suite and the GOMC simulation engine. The MoSDeF libraries also supports various simulation engines, including Cassandra, GOMC, GROMACS, HOOMD-blue, and LAMMPS. The MoSDeF-GOMC and MoSDeF libraries permit reproducibility simulations across a wide range of simulation engines, eliminating the need to be an expert in every simulation engine to replicate or expand upon the existing research. These software packages can auto-produce a variety of different chemical systems, permitting large-scale screening of chemicals and materials using signac to manage the simulations, data, and analysis.