Welcome to the MoSDeF tutorial at FOMMS 2024
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 workflows, that is, workflows that can utilize multiple simulation engines to at different steps of the simulation process, and simulate systems at multiple scales, e.g, ab initio, atomistic, coarse-grained, and more. Most importantly, the MoSDeF software suite trivializes the distribution of the system's initialization, and parameterization process, ensuring their reproducibility by the general community.
The MoSDeF software suite consist of three core libraries, namely mBuild, Foyer, and GMSO. Each library is dedicated 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 encounter 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- Unpublished codes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 the systems, and write out the paramerized system 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, FAIR (Findable, Accesible, Interoperable, and Reusable) data management.
Each of the notebooks has ~2-4 minutes of software installation cells at the top. We recommend running these while we're getting oriented to each workbook
These tutotial workflows are designed to be easily accessible on Google Colab. Users can access these notebooks through the below links:
To run cells in an open notebook, press Shift+Return to execute a selected code block. In each notebook there are a few cells at the top that install required dependencies. It is known that the condacolab installation cell stops the colab kernel- Just wait for it to restart and run the subsequent cell.
If you clone this repository to your local laptop you won't need to use the condacolab installation cells and can install dependencies directly with conda or mamba.
More in-depth MoSDeF tutorials: https://github.com/mosdef-hub/mosdef_tutorials
Example MoSDeF workflow: https://github.com/mosdef-hub/mosdef-workflows
Documentations:
- https://mbuild.mosdef.org/en/stable/
- https://foyer.mosdef.org/en/stable/
- https://gmso.mosdef.org/en/stable/
