2024-06-10 Mitchell/Wagner Check-in meeting notes

Participants

@Josh Mitchell
@Jeffrey Wagner

Discussion topics

Item	Notes

Item

Notes

General updates

JW –
- We’re working with PEastman/OpenMM to spec out improvements to PDBFixer, likely including support for more residues (hopefully incl custom residues) and possibly assignment of bond orders+formal charges.

Video uploads

Zenodo descriptions

JM ORCID - 0000-0002-8246-5113

JW ORCID 0000-0001-6448-0873

2024 OpenFF SMIRNOFF Mini-workshop

The "SMIRNOFF Force Fields and You" OpenFF Mini-workshop, presented by Josh Mitchell.

SMIRNOFF is an open format for specifying molecular mechanics force fields directly for the chemistry of a target molecule, rather than indirectly through abstractions like atom types. Unlike other force field formats, SMIRNOFF describes not only the parameters of the force field, but also the chemistries to which those parameters should be applied.

This workshop introduces the SMIRNOFF format to familiar MD practitioners and describes how a system can be parametrized from a SMIRNOFF force field for a number of different MD engines. We hope to get both users and developers of molecular mechanics force fields excited about this game changing format.

Goals: Attendees will learn…

That SMIRNOFF force fields are maps from arbitrary chemistry to a potential energy function
That SMIRNOFF force fields can be combined to provide general coverage AND specific detail
The basic format of a SMIRNOFF force field
How to apply a collection of SMIRNOFF force fields to a ready-to-simulate box in PDB format
That anyone can publish their SMIRNOFF force field (big or small) anywhere that distributes Python packages

Non-goals:

How to prepare an MD system - this workshop focuses on force fields themselves and emphasizes conceptual understanding over application
Configuring BespokeFit for uses beyond Sage

Assumed knowledge:

Basic working understanding of MD, force fields, structural biology
Experience preparing MD systems and running simulations
Some experience with Python helpful but not required

2024 OpenFF Protein Preparation Mini-workshop

The "Protein Preparation and You" OpenFF Mini-workshop, presented by Josh Mitchell.

Today, Jupyter notebooks are everything you need to prepare a molecular dynamics simulation. Not only do they provide a unified interface to all the tools needed to prepare and visualize a simulation, they also provide an easy way to record, repeat, and even publish your workflow, including any alterations needed for a particularly stubborn system.

This workshop covers the preparation of a protein system from a structure downloaded from the PDB, entirely in the Jupyter notebook, complete with 3D visualizations at every step of the way. We hope to make it accessible even to new MD practitioners, assuming they have some familiarity with Python.

2024 OpenFF Vignettes Mini-workshop

The "Things to Make and Do with OpenFF" Mini-workshop, presented by Josh Mitchell of OpenFF.

The OpenFF software ecosystem is a flexible and highly programmable collection of tools that is easy to interface with both cheminformatics suites and MD engines. At the same time, it is oriented towards detecting and rejecting molecular systems that don’t make chemical sense, or that are ambiguous in the chemistry they represent. This makes it quite powerful and pleasant to use for a wide range of biomolecular simulation tasks.

This workshop will display this flexibility by demonstrating a variety of unusual uses of the OpenFF ecosystem and its software neighbors. These “vignettes” will run the gamut from useful to cute, robust to experimental, and simple to complex. Rather than focus on the details of how each is accomplished, vignettes will each be demonstrated quickly alongside a brief highlight of the relevant part of the ecosystem.

You can install the software to run this example and execute the notebook on your own linux or mac computer. This requires an installation of Mamba, Micromamba, or similar conda-forge compatible package manager (see https://docs.openforcefield.org/en/latest/install.html).

First, download the workshop zip file from the zenodo data below, extract the zip file and open a terminal in the extracted directory. Then, create the environment:

mamba env create -n vignettes-workshop -f examples_env.yml

And run Jupyter Lab in the new environment:

mamba run -n vignettes-workshop jupyter lab

Open Force Field examples page: https://docs.openforcefield.org/examples

Open Force Field documentation: https://docs.openforcefield.org

Open Force Field technical support: support@openforcefield.org

Twitter: https://twitter.com/openforcefield

GitHub: https://github.com/openforcefield

Acknowledge

National Institutes of Health

NIH R01 GM132386

Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug design