Development and benchmarking of Open Force Field 2.0.0---the Sage small molecule force field

Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang L-P, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL
Journal of Chemical Theory and Computation 19:3251, 2023 [DOI] [chemRxiv] [GitHub] [examples]

We present a new generation of small molecule force field for molecular design from the Open Force Field Initiative fit to both quantum chemical and experimental liquid mixture data

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

Horton JT, Boothroyd S, Wagner W, Mitchell JA, Gokey T, Dotson DL, Behara PK, Ramaswamy VK, Mackey M, Chodera JD, Anwar J, Mobley DL, and Cole DJ
Journal of Chemical Informatics and Modeling 62:22, 2022 [DOI]

We describe an automated pipeline for generating tailored force field parameters for small molecules using quantum chemical or quantum machine learning potentials.

Improving force field accuracy by training against condensed-phase mixture properties

Boothroyd S, Madin OC, Mobley DL, Wang L-P, Chodera JD, and Shirts MR
Journal of Chemical Theory and Computation 18:3577, 2022 [DOI] [GitHub]

We use a new automated framework for physical property evaluation and fitting to show how molecular mechanics force fields can be systematically improved by fitting to condensed phase properties.

Capturing non-local through-bond effects in molecular mechanics force fields: II. Using fractional bond orders to fit torsion parameters

Stern CD, Maat J, Dotson DL, Bayly CI, Smith DGA, Mobley DL, and Chodera JD
preprint: [bioRxiv]

We show how the Wiberg Bond Order (WBO) can be used to accurately interpolate torsional profiles for molecular mechanics force fields, which holts the potential for drastically reducing the complexity of these force fields while increasing their ability to generalize and accurately treat complex druglike molecules such as kinase inhibitors.

Quantum chemistry common driver and databases (QCDB) and quantum chemistry engine (QCEngine): Automation and interoperability among computational chemistry programs

Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, Hurtado AG, Kraus P, Kruse P, Lee SJR, Misiewicz JP, Naden LN, Ramezanghorbani F, Scheurer M, Shriber JB, Simmonett AC, Steinmetzer J, Wagner JR, Ward L, Welborn M, Altarawy D, Anwar J, Chodera JD, Dreuw A, Kulik HJ, Liu F, Martinez TJ, Matthews DA, Schaefer III HF, Sponer J, Turney JM, Wang L-P, De Silva N, King RA, Stanton JF, Gordon MS, Windus TL, Sherrill CD, Burns LA
Journal of Chemical Physics} 155:204801, 2021 [DOI]

We describe a new community-wide approach to interoperability for quantum chemistry packages that will enable large-scale applications such as next-generation machine learning for chemistry and automated force field construction for drug discovery.

Development and benchmarking of Open Force Field v1.0.0, the Parsley small molecule force field

Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C Bannan, Trevor Gokey, Victoria T Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R Shirts, Michael Gilson, John D. Chodera, Christopher I Bayly, David Mobley, Lee-Ping Wang
Preprint ahead of publication: [chemRxiv] [force fields] [Open Force Field Initiative]

We present a new, modern small molecule force field for molecular design from the Open Force Field Initiative, a large industry-academic collaboration that focuses on open science, open data, and modern open source infrastructure.

Escaping atom types in force fields using direct chemical perception

David L. Mobley, Caitlin C. Bannan, Andrea Rizzi, Christopher I. Bayly, John D. Chodera, Victoria T Lim, Nathan M. Lim, Kyle A. Beauchamp, Michael R. Shirts, Michael K. Gilson, Peter K. Eastman.
Journal of Chemical Theory and Computation 14:6076, 2018 [DOI] [bioRxiv]

We describe the philosophy behind a modern approach to molecular mechanics forcefield parameterization, and present initial results for the first SMIRNOFF-encoded forcefield: SMIRNOFF99Frosst.