Workshops
Please see below the list of the past and upcoming workshops organized by the Open Force Field Initiative.
6th Open Force Field Workshop
The 6th Open Force Field Workshop was held as a part of the 2023 Open Molecular Software Foundation Symposium.
May 14, 2023 | part of the 2023 OMSF Symposium
These talks are available on our YouTube Channel
5th Open Force Field Workshop
The 5th Open Force Field Workshop was held as a series of online presentations over several months in 2022.
June - October, 2022 | Online Workshop Series
These talks are available on our YouTube Channel
Keynote
June 28, 2022
David Mobley
Jeff Wagner
Lily Wang
Diego Nolasco
(https://doi.org/10.5281/zenodo.6774451)
Interchange Showcase
Matt Thompson This session covers the current state of Interchange development and future plans. The example code explores the API points for creating, inspecting, modifying, combining, and exporting parameterized molecular systems using the new Interchange object, and shows examples of how Interchange can be tied into larger workflows.
(https://doi.org/10.5281/zenodo.7121172) Watch on YouTube
Biopolymer Showcase
September 27, 2022
Josh Mitchell A session on biopolymer support in OpenFF Toolkit 0.11, showing advanced usage by parametrizing a protein with a post-translational modification (PTM). This workshop demonstrates loading and parametrizing biopolymers with the OpenFF Toolkit, including a preview of support for a non-canonical amino acid. We introduce the Toolkit’s new biopolymer support, and then demonstrate a way to apply a post-translational modification. We look at optimizing charge generation by transferring charges generated from a simpler molecule to our new peptide, and then simulate it in OpenMM!
(https://doi.org/10.5281/zenodo.7307172) Watch on Youtube
BespokeFit Showcase
October 19th & 25th, 2022
Josh Mitchell 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
4th Open Force Field Workshop
The 4th Open Force Field Workshop was held as a series of online presentations over several months in 2021.
June - September, 2021 | Online Workshop Series
These talks are available on our YouTube Channel.
Keynote
June 11th, 2021
Simon Boothroyd
David Mobley
Jeff Wagner
(https://doi.org/10.5281/zenodo.4950029)
Benchmarking
September 1st, 2021
Lorenzo D’Amore Large scale benchmarking of force fields in protein-ligand free energy calculations
(https://doi.org/10.5281/zenodo.5369857)
Bespoke Fitting
September 8th, 2021
Joshua Horton Automated Bespoke Parameters for OpenFF
3rd Open Force Field Workshop
The Third Open Force Field Workshop was initially as an in-person gathering in Boston on May 4-5, 2020, but this meeting was cancelled due to the Covid-19 outbreak. This in-person meeting was replaced by a virtual meeting on the same dates. We decided to slightly experiment with the workshop format by making most of the content available before the meeting for asynchronous consumption.
May 4-5, 2020 | Virtual meeting
We hosted the Third Open Force Field Consortium Workshop on May 4-5, 2020 as a virtual meeting. This virtual meeting replaced the planned in-person gathering in Boston. All talks were pre-recorded and the meeting time was focused on discussions and future planning. David Cerutti, who has joined the Open Force Field Initiative as a senior scientist to assist with development of biopolymer force fields funded by the NIH grant, gave a virtual keynote and a brief summary of his talk before discussion. The main aim of this format was to make this virtual meeting more interactive, and hopefully, more productive.
Talks and discussions
The recording sessions were open to all meeting attendees to join in real time, and shared on our YouTube channel on the same day. To access presentation slides and better video quality, download provided content from Zenodo. All talks with links to YouTube and Zenodo are provided below together with meeting notes from discussion sessions.
Agenda
Talks
The list of talks grouped by theme:
Introduction
David Mobley: Current status of OpenFF and our near-term roadmap
YouTube | Zenodo
Infrastructure Update
Daniel Smith: QC Archive infrastructure updates
YouTube | Zenodo
Jeffrey Wagner: Updates on core OpenFF infrastructure
YouTube | Zenodo
Chaya Stern: Capturing non-local through-bond effects when fragmenting molecules for QC torsion scans
YouTube | Zenodo
Force Field Updates
Jessica Maat: Training dataset selection
YouTube | Zenodo
Hyesu Jang: Update on Parsley minor releases (openff-1.1.0, 1.2.0)
YouTube | Zenodo
Benchmarking (Parsley)
Victoria Lim: Benchmark assessment of molecular geometries and energies from small molecule force fields
YouTube | Zenodo
David Hahn: Parsley parameters in protein-ligand binding free energy calculations
YouTube | Zenodo
Next Steps / Ongoing Studies
Simon Boothroyd: Which physical properties should we be optimizing against?
YouTube | Zenodo
Jeffry Setiadi: Host-guest binding calculations with OpenFF evaluator
YouTube | Zenodo
Michael Gilson: How Many Lennard-Jones Atom Types Does a Force Field Need?
YouTube | Zenodo
Future Directions
Owen Madin: Future directions in parameterization: enabling Bayesian inference with surrogate modeling
YouTube | Zenodo
Yuanqing Wang: Near-chemical accuracy at molecular mechanics speed: Neural parameterization of extended force field using graph nets
YouTube | Zenodo
Yuanqing Wang: Graph Nets for partial charge prediction
This is a previously given webinar, but relevant for this context.
YouTube | Zenodo
Biopolymers / Keynote
David Cerutti: Strategies for ab initio Biomolecular Force Field Development
YouTube | Zenodo
Discussion sessions (May 4-5, 2020)
Please note that all times refer to the Pacific Time Zone.
Day 1 (May 4, 2020)
| Time | Discussion |
|---|---|
| 7.00 am | Session I: Current status and performance of Open Force Fields and infrastructure - David Mobley: Introduction and a brief recap from talks - Discussion Relevant talks (by theme): Introduction, Infrastructure, Force field updates, Benchmarking |
| 8.30 am | Break |
| 8.45 am | Session II: Roadmaps - Science - Infrastructure - Data Relevant talks (by theme): Infrastructure, Force Field Updates, Next Steps |
Day 2 (May 5, 2020)
| Time | Discussion |
|---|---|
| 7.00 am | Session I: Biopolymer force fields - Michael Shirts: Aims for the NIH-funded bioplymer force fields - David Cerutti: Strategies for ab initio biomolecular force field development YouTube | Zenodo - Discussion |
| 8.30 am | Break |
| 8.45 am | Session II: Future directions - John Chodera: Future directions for the Open Force Field Initiative Relevant talks (by theme): Future Directions |
| 8.30 am | Wrap-up discussion |
Recording sessions
Please note that all times refer to the Pacific Time Zone.
Day 1 (Apr 27, 2020)
| Time | Speaker | Talk |
|---|---|---|
| 8.30 am | Chaya Stern | Capturing non-local through-bond effects when fragmenting molecules for QC torsion scans Wiberg bond orders (WBO) are sensitive to remote substituents and can be used as a surrogate for torsion energy barrier heights. Here we use WBOs to assess the robustness of fragmentation schemes and identify conjugated bond sets. YouTube | Zenodo (video + slides) |
| 9.00 am | Daniel Smith | QC Archive infrastructure updates Highlights on feature improvements, data artifact generation, and data visualization on the QCArchive website. YouTube | Zenodo (video + slides) |
| 9.30 am | Jeffrey Wagner | Updated on core OpenFF infrastructure New features in the Open Force Field Toolkit, and other developments in core software. YouTube | Zenodo (video + slides) |
Day 2 (Apr 28, 2020)
| Time | Speaker | Talk |
|---|---|---|
| 8.30 am | David Mobley | Current Status of OpenFF and our Near-Term Roadmap I’ll briefly discuss where we are now relative to where we were at the last meeting, and what our near-term horizon looks like for future developments. This will include a brief overview of force field and infrastructure topics of particular interest, with more details to come from other speakers. YouTube | Zenodo (video + slides) |
| 9.00 am | Victoria Lim | Benchmark assessment of molecular geometries and energies from small molecule force fields I will present my results on a comparison of several small molecule force fields in terms of how well they can reproduce geometries and relative conformer energies with respect to QM reference data. YouTube | Zenodo (video + slides) |
| 9.30 am | Jessica Maat | QM data selection QM data selection for OpenFF-1.2.0 force field. Discussion on how the data set was selected to improve the new force field release. YouTube | Zenodo (video + slides) |
Day 3 (Apr 29, 2020)
| Time | Speaker | Talk |
|---|---|---|
| 9.00 am | Simon Boothroyd | Which physical properties should we be optimizing against? An update on refitting the non-bonded (LJ) parameters of the OpenFF force fields against physical property data. A focus is given to exploring which types of physical properties yield the largest improvement in force field performance. YouTube | Zenodo (video + slides) |
| 9.30 am | David Hahn | Parsley parameters in protein-ligand binding free energy calculations QM data selection for OpenFF-1.2.0 force field. Discussion on how the data set was selected to improve the new force field release. YouTube | Zenodo (video + slides) |
Day 4 (Apr 30, 2020)
| Time | Speaker | Talk |
|---|---|---|
| 8.30 am | Michael Gilson | How many Lennard-Jones atom types does a force field need? Results of a data-driven investigation. YouTube | Zenodo (video + slides) |
| 9.00 am | Jeffry Setiadi | Host-guest binding calculations with OpenFF Evaluator Current status of pAPRika integration with OpenFF Evaluator. YouTube | Zenodo (video + slides) |
Day 5 (May 1, 2020)
| Time | Speaker | Talk |
|---|---|---|
| 8.30 am | Owen Madin | Future directions in parameterization: Enabling Bayesian inference with surrogate modeling I’ll discuss our interest in using Bayesian inference to make decisions about non-bonded interactions, and our planned usage of surrogate models to achieve this. I’ll use the 2CLJQ system as a case study. YouTube | Zenodo (video + slides) |
| 9.00 am | Yuanqing Wang | Near-Chemical Accuracy at Molecular Mechanics Speed: Neural Parameterization of Extended Force Field using Graph Nets By using graph neural networks capable of automatically perceiving chemical environment and directly producing parameters for a fast classical potential, we show it is possible to flexibly assign parameters to near-arbitrary biomolecular systems while achieving near-quantum chemical accuracy with molecular mechanics speed. YouTube | Zenodo (video + slides) |
| 9.30 am | Hyesu Jang | Update on Parsley minor releases (OpenFF-1.1.0 and 1.2.0) Valence parameter re-fitting was done with (1) parameter definition adjustments and (2) newly designed QM training set, followed by performance validation. YouTube | Zenodo (video + slides) |
2nd Open Force Field Workshop
We hosted the Second Open Force Field Workshop again in La Jolla, CA on August 30-31, 2019. The first two days of the workshop focused on the progress update and future planning of OpenFF efforts in Year 2. The workshop was extended for another day (Sep 1), which was reserved for OpenFF team discussions, but open to interested Industry Partners. The venue was provided by the Skaggs School of Pharmacy and Pharmaceutical Sciences at UCSD campus.
Aug 30-31, 2019 | La Jolla, California
The meeting was open to Consortium members and collaborators, and parts of the meeting were recorded for posting online with accompanying slides. Watch the videos from this workshop on YouTube and access presentation slides on Zenodo.
Please see the full program below:
Agenda
The proposed agenda might be subjected to minor changes before the event.
Day 1 (Aug 30)
| Time | Event | Speaker |
|---|---|---|
| 7.30 - 8.15 | _ Breakfast _ | |
| — | — | — |
| 8.15 - 8.30 | Welcome | OpenFF PIs |
| 8.30 - 9.15 | Progress and status for the OpenFF small molecule force field | Video |
| 9.15 - 10.00 | OFF Toolkit Showcase: Current capabilities | Video |
| 10.00 - 10.30 | Discussion of progress and current status | Video |
| 10.30 - 11.00 | _ Coffee break _ | |
| 11.00 - 11.30 | Parameterization perspective I: Parameterization methodology | Video |
| 11.30 - 12.00 | Parameterization perspective II: Property Calculator | Video |
| 12.00 - 12.15 | Parameterization perspective III: Data for parameterization and validation - QCArchive | Video |
| 12.15 - 12.30 | Parameterization perspective IV: Data for parameterization and validation - Physical properties | Video |
| 12.30 - 13.30 | _ Lunch _ | |
| 13.30 - 14.30 | Open discussion of the morning talks: Feedback and outlook for Y2, near-term planning, challenges | Chair: Mike Gilson |
| 14.30 - 15.15 | Breakout session I: Force field assessment - physical properties of small molecules | Chair: Michael Shirts |
| 14.30 - 15.15 | Breakout session I: Chemical perception / addition of new parameters / chemical space coverage | Chair: David Mobley |
| 15.15 - 15.30 | Breakout session reports | |
| 15.30 - 16.00 | _ Coffee break _ | |
| 16.00 - 16.45 | Breakout session II: Force field assessment - protein-ligand free energies - [discussion summary] | Chair: John Chodera |
| 16.45 - 17.00 | Breakout session II: Parameter definition, dataset selection, optimization strategies | Chair: Lee-Ping Wang |
| 18.30 | **_Workshop dinner:_** ** Rock Bottom Brewery** | |
Day 2 (Aug 31)
| Time | Event | Speaker |
|---|---|---|
| 7.45 - 8.30 | _ Breakfast _ | |
| — | — | — |
| 8.30 - 9.30 | Advisory Board meeting (closed) | |
| 9.30 - 10.15 | Future parameterization perspective: Plan for Year 2 and beyond | Video |
| 10.15 - 10.45 | _ Coffee break _ | |
| 10.45 - 11.30 | ANI-1 and neural net potentials | Video |
| 11.30 - 12.30 | Open discussion: Anticipated next force field development steps | Video |
| 12.30 - 13.00 | Concluding remarks and future outlook | |
| 13.00 - 14.00 | _ Lunch _ | |
| 14.00 - 15.15 | Free discussion: Short-term and long-term plans for OpenFF | Concurrent 1:1 sessions for Partners with J. Wagner |
| 15.15 - 15.45 | _ Coffee break _ | |
| 15.45 - 17.00 | Free discussion: ML perspectives in OpenFF | Concurrent 1:1 sessions for Partners with J. Wagner |
Day 3 (Sep 1)
Internal OpenFF team discussions and planning session.
| Time | Event | Moderator |
|---|---|---|
| 8.30 - 9.00 | _ Breakfast _ | |
| — | — | — |
| 9.00 - 10.30 | Internal organization and project structure | Karmen Condic-Jurkic |
| 10.30 - 11.00 | _ Coffee break _ | |
| 11.00 - 13.00 | Roadmap planning and deliverables for Year 2 | Karmen Condic-Jurkic |
| 13.00 - 14.00 | _ Lunch _ | |
| 14.00 - 15.00 | Summary | |
| 15.00 - 17.00 | Free discussion and departure | |
1st Open Force Field Workshop
The First Open Force Field Workshop was held in La Jolla, CA on January 7-8, 2019. The meeting was open to Consortium members and collaborators, and parts of the meeting were recorded for posting online. Watch the videos from this workshop on YouTube and access presentation slides on Zenodo.
Jan 7-8, 2019 | La Jolla, California
Please see the full program below:
Agenda
Comments and questions for discussion during the workshop are invited in the Slack channels indicated after each topic; e.g, #project-planning for "Roadmap overview".
Jan 7
Research topics: 45 min talk + 15 min discussion
| Time | Event | Speaker | Slack channel |
|---|---|---|---|
| 7.45 - 8.00 | Introduction [PDF] [Video] | Gilson | |
| — | — | — | — |
| 8.00 - 8.30 | Roadmap overview [DOI] [Video] | Shirts | #project-planning |
| 8.30 - 9.30 | Short-term parameter optimization strategy: ForceBalance [DOI] [Video] | Wang | #forcebalance |
| 9.30 - 10.00 | Coffee break | ||
| #random | |||
| 10.00 - 11.00 | Long-term parameter optimization strategy: Bayesian Fitting [DOI] [Video] | Chodera | #bayesian-inference |
| 11.00 - 12.00 | Chemical perception and SMIRNOFF typing [DOI] [Video] | Mobley/Bannan | #smirnoff |
| 12.00 - 1.00 | Torsion fitting and fragmentation [DOI] [Video] | Chodera/Wang | #torsions |
| 1.00 - 2.00 | Lunch (catered) | ||
| 2.00 - 2.30 | Group discussion to define ad hoc breakouts and breakout leaders/note-takers | ||
Proposed Breakout Session 1 : typing via chemical perception, torsion fitting
Proposed Breakout Session 2 : useful physical property data, parameter fitting ||
| Time | Event | Speaker | Slack channel |
|---|---|---|---|
| 2.30 - 3.00 | Breakout Session 1 | ||
| 3.00 - 3.30 | Coffee break | ||
| #random | |||
| 3.30 - 4.00 | Breakout Session 2 | ||
| 4.00 - 5.00 | Reconvene for breakout reports and all-hands discussions | ||
Breakout session notes: Benchmarking Accuracy [PDF] |
Breakout session notes: Property calculation framework [PDF] |
Breakout session notes: Use cases [PDF] |
| Time | Event | Speaker | Slack channel |
|---|---|---|---|
| 5.00 - 5.15 | Roadmap recap and discussion (reviewing Slack input from remote attendees) | ||
| #project-planning | |||
| 6.00 | Group dinner in La Jolla at Rock Bottom Brewing | ||
Jan 8
Research topics 45 min talk + 15 min discussion
| Time | Event | Speaker | Slack channel |
|---|---|---|---|
| 8.00 - 9.00 | Charge models [DOI] [Video] | Schauperl | #charge-models |
| — | — | — | — |
| 9.00 - 10.00 | Fitting non-torsion valence terms [DOI] [Video] | Mobley/Wang | #valence |
| 10.00 - 10.30 | Coffee break | ||
| #random | |||
| 10.30 - 11.30 | Software architecture and infrastructure [DOI] [Video] | Wagner | #infrastructure |
| 11.30 - 12.30 | Fitting condensed-phase properties [DOI] [Video] | Chodera/Shirts | #propertycalculator |
| 12.30 - 1.30 | Lunch (catered) | ||
| 1.30 - 2.00 | Group discussion to define ad hoc breakouts and breakout leaders/note-takers | ||
Proposed Breakout Sessions: electrostatics, software preview / toolkit hands-on ||
| Time | Event | Speaker | Slack channel |
|---|---|---|---|
| 2.00 - 4.00 | Breakout Session (with coffee) | ||
| 4.00 - 5.00 | Reconvene and wrap-up discussion | ||
Breakout session notes: neural network potentials [PDF] |