2023-10-11 Flatiron Institute / Shirts Group

Prelim discussion of FI desires

PDR

• Vikram Mulligan is creating a software package called Masala

• FI wants to continue working on foldamers and other exotic chemistry

• FI would like to use masala for this

• Masala links to Rosetta

  • is written in a way that should be easier to interoperate with other packages

    • defines its own API in a machine-readable way

  • Masala has a plug-in architecture – does run-time linking

  • Goal: be able to define new energy functions as a plug-in to masala

  • Application: e.g. benchmarking

• If we were to re-implement any component to optimize performance, would OpenFF want it back?

Introduction to OpenFF

JE

• SMIRNOFF

  • https://pubs.acs.org/doi/10.1021/acs.jctc.8b00640

• Toolkit

  • Cookbook: Every way to make a Molecule — OpenFF Toolkit 0.16.7+d20241213 documentation

• Interchange

• Sage force field

More details about OpenFF

MS

• Shirts group has generalized polymer loading in the OpenFF Toolkit.

  • https://chemrxiv.org/engage/chemrxiv/article-details/64cb1d784a3f7d0c0d8077c1

• Plug-in infrastructure

  • Danny Cole swapping out LJ double-exponential instead of 6-12

Next steps

• Next week’s meeting will be science

  • each side gives a 20 minute high-level presentation of their scientific interests and goals

• After that, we can set up a meeting with infrastructure team about plug-in architecture.