MoSDeF

The MoSDeF tools have been designed to facilitate the hierarchical construction of both atomistic and coarse-grained system configurations, the application of classical force fields (i.e., atom-typing), encapsulation of chemical topology information, and the generation of input files for a variety of molecular dynamics and Monte Carlo simulation engines, including LAMMPS, GROMACS, HOOMD-Blue, Cassandra, and GOMC.

TRUE Simulations
                        Through the MoSDeF integrated framework, the exact procedures used to set up and perform
                        simulation workflows and associated metadata (i.e. the provenance) can be scripted,
                        encapsulated, version-controlled, preserved, and later reproduced by other researchers. This
                        allows molecular simulation studies to be conducted and published in a manner that is TRUE
                    : “Transparent, Reproducible, Usable by others, and Extensible
                    .” The following paper highlights these principles in details.
                    
Flexibility
                        System construction and initialization are performed in a simulation engine agnostic fashion,
                        allowing users to use a single set of scripts to generate inputs for a variety of different
                        simulation engines.
                        
                        Because systems are constructed in a hierarchical, scriptable fashion, modifications to system
                        chemistry can be easily made, allowing for screening over chemical space.
                    
Community
                        MoSDeF is designed to allow system construction scripts to be easily made into easy to
                        distribute libraries; similarly, forcefield files contain parameters and their usage rules that
                        can be easily shared and version controlled.
                    
Join the mailing listMosdef Gitter Github Organization

The easiest way to get started with MoSDeF is to go through our tutorials. Below is a curated list of quick start guides:

Details	GitHub	Binder
MosDeF Tutorials: Curated tutorials for the MosDeF Framework
mBuild Tutorials: Curated tutorials for mBuild
Foyer Tutorials: Curated tutorials for Foyer

mBuild
A hierarchical, component based molecule builder
starmore
Foyer
A package for atom-typing as well as applying and disseminating forcefields
starmore
GMSO
Flexible storage of chemical topology for molecular simulation
starmore

Other MoSDeF Projects

Forcefield Template: A template repo for disseminating force fields with foyer

Nanoparticle Optimization: Deriving potentials for coarse-grained nanoparticles via potential-matching

MultiState Boltzmann Inversion (MS-IBI): Manage and run pair potential optimizations using multistate iterative Boltzmann inversion

MoSDeF Tutorials: A set of tutorials to introduce new users to the MoSDeF (Molecular Simulation Design Framework) toolkit

mBuild Tutorials: A set of tutorials to introduce new users to mBuild

foyer Tutorials: A set of tutorials to introduce new users to foyer

Projects Using MoSDeF

MoSDeF Cassandra: MoSDeF compatible wrapper for Cassandra Monte Carlo code

MoSDeF GOMC: MoSDeF compatible wrapper for GPU Optimized Monte Carlo (GOMC) code

planckton: Reproducible exploration of organic photovoltaic morphology self-assembly using molecular dynamics.

MosDeF-CP2K-Writer: Scripted control and better documentation of CP2K simulations in accord with the goals of the CSSI MoSDeF project

GMSO Showcase: Interactive demo/tutorial of current GMSO features and design decisions.

GRiTS: GRiTS Reduces/Restores Topology with SMILES

MoSDeF Workflows: Sample molecular simulation workflows using MoSDeF

Also, checkout projects from our collaborators: Boise State | Michigan | Notre Dame | Wayne State.

MoSDeF is supported by a Cyberinfrastructure for Sustained Scientific Innovation (CSSI) grant funded by the National Science Foundation Office of Advanced Cyberinfrastructure.

                        
                        Peter T.
                            Cummings,
                        1835874
                    
                        Clare
                            McCabe,
                        1835874
                    
                        Akos
                            Ledeczi,
                        1835874
                    
                        Eric Jankowski,
                        1835593
                    
                        Arthi Jayaraman,
                        1835613
                    
                        Jeremy Palmer,
                        1835560
                    
                        Sharon
                            C. Glotzer,
                        1835612
                    
                        Joern
                            Ilja. Siepmann,
                        1835067
                    
                        Edward J.
                            Maginn,
                        1835630
                    
                        Jeffrey J.
                            Potoff,
                        1835713

Molecular Simulation Design Framework (MoSDeF)

TRUE Simulations

Flexibility

Community

Join the mailing list

Mosdef Gitter

Github Organization

Quick Start

Quick Peek

Foundational MoSDeF Repositories

Other MoSDeF Projects

Projects Using MoSDeF

Collaborators

Get Involved