BespokeFit Showcase - 5th Open Force Field Workshop (2022)
Channel: Open Force Field Initiative
Date: 2022-11-16

An example session on using BespokeFit and incorporating it into your workflows. BespokeFit is an OpenFF package for automatically optimising torsion parameters for arbitrary small molecules. We present a worked example taking a ligand through optimization and simulation

This workshop was recorded on the 19th and 25th of October 2022 and has been edited down to size. We'd love to hear your thoughts on whether this editing improves your viewing experience!

The materials to run this workshop can be downloaded here: https://gist.github.com/Yoshanuikabundi/2860cf864ed1658ceec466bfb599e3fe

To run, first install Conda, then download the materials from the Gist above, either from the “Download ZIP” button or by cloning with Git, and finally follow the instructions in README.md. Alternatively, the notebook can be followed and executed online on Binder: https://mybinder.org/v2/gist/Yoshanuikabundi/2860cf864ed1658ceec466bfb599e3fe/HEAD

Chapters:
00:00 Intro
00:23 Running Bespoke Executor
02:42 How BespokeFit works
03:50 Caching and Fragmentation 
10:26 Configuring BespokeFit
20:11 BespokeFit CLI
24:53 The magic of BespokeFit
25:24 Notebook 2: Protein-ligand simulation
27:11 Loading and inspecting a BespokeFit force field
30:47 System prep and simulation
35:11 Summing up 

Open Force Field documentation: https://docs.openforcefield.org
Open Force Field technical support: support@openforcefield.org
Discourse: https://discourse.openforcefield.org/
Twitter: https://twitter.com/openforcefield
GitHub: https://github.com/openforcefield