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.
mosdef-slideshow

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.

True Simulations

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.


Flexibility

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.

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community

Quick Start

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 Binder
mBuild Tutorials: Curated tutorials for mBuild Binder
Foyer Tutorials: Curated tutorials for Foyer Binder

Quick Peek

Foundational MoSDeF Repositories

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
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.

Collaborators


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

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Contributions are welcome! Just fork any of the projects and submit some pull requests or develop your own custom extensions.