Welcome to the MoSDeF tutorial at the CECAM Flagship Workshop: Proposal FAIR and TRUE Data Processing for Soft Matter Simulations.

The Molecular Simulation Design Framework, or MoSDeF, is a collaborative project focused on developing an open-source software suite to assist with the preparation of chemical/biological systems for molecular simulation. The framework strives to create tools that are:

• Non-specific
• Force field agnostic
• Engine agnostic

These principals allow for the creation of more diverse workflow, that is, utilizing multiple simulation engines to perform each steps of the simulation process and simulate systems at multiple scales, e.g, ab initio, atomistic, coarse-grained. Most importantly, the MoSDeF software suite trivializes the distribution of the system initialization and parameterization process, to ensure their reproducibility by the general community.

The MoSDeF software suite consist of three core libraries, namely mBuild, Foyer, and GMSO. Each library dedicates to handle a certain step of the chemical system initialization process, as summarized in the figure below.

Transparent, Reproducible, Usable by others, and Extensible (TRUE) are four criteria for published computational simulation research introduced by Thompson et al. The TRUE criteria are introduced to address the (ir)reproducibility issues in the community, which, in many cases, can be attributed to:

• Human error
• Incomplete reports of simulation workflow
• Unpublished codes

The MoSDeF provides necessary tools to automate the simulation workflow in a scriptable manners, eliminating unnecessary manual interaction with the established workflow, and simplify the distribution of codes utilized for the system initialization process, and assist with the adherence to the TRUE criteria.

In this tutorial, we will walk through a series of simulation workflows, all using MoSDeF to create the chemical/biological systems, parameterize, and write out to different file formats that can be taken in by various simulation engines. Through these workflow, we want to demonstrate how our libraries can be used to design TRUE (Transferable, Reproducible, Usable-by-other, and Extensible) studies, and ensure FAIR (Findable, Accesible, Interoperable, and Reusable) data management.

These tutotial workflows are designed to work on Google Colab. User can access these notebooks through the below links:

• Water Adsorption in Graphene Slitpore
• Biomolecule
• Polymer
• Solvated Surface

To setup and run these workflow locally, please follow the Local Installation Instructions.

More in-depth MoSDeF tutorials: https://github.com/mosdef-hub/mosdef_tutorials

Example MoSDeF workflow: https://github.com/mosdef-hub/mosdef-workflows

Documentation:

- https://mbuild.mosdef.org/en/stable/
- https://foyer.mosdef.org/en/stable/
- https://gmso.mosdef.org/en/stable/