open force field

An open and collaborative approach to better force fields

Webinars
Workshops

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.

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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.

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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

(https://doi.org/10.5281/zenodo.7340156) Watch on YouTube


4th Open Force Field Workshop

The 4th Open Force Field Workshop was held as a series of online presentations over several months in 2021.

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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

(https://doi.org/10.5281/zenodo.5495926)


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.

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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)

Meeting notes - Day 1

TimeDiscussion
7.00 amSession 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 amBreak
8.45 amSession II: Roadmaps
- Science
- Infrastructure
- Data
Relevant talks (by theme): Infrastructure, Force Field Updates, Next Steps

Day 2 (May 5, 2020)

Meeting notes - Day 2

TimeDiscussion
7.00 amSession 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 amBreak
8.45 amSession II: Future directions
- John Chodera: Future directions for the Open Force Field Initiative
Relevant talks (by theme): Future Directions
8.30 amWrap-up discussion

Recording sessions

Please note that all times refer to the Pacific Time Zone.

Day 1 (Apr 27, 2020)

TimeSpeakerTalk
8.30 amChaya SternCapturing 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 amDaniel SmithQC Archive infrastructure updates
Highlights on feature improvements, data artifact generation, and data visualization on the QCArchive website.
YouTube | Zenodo (video + slides)
9.30 amJeffrey WagnerUpdated 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)

TimeSpeakerTalk
8.30 amDavid MobleyCurrent 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 amVictoria LimBenchmark 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 amJessica MaatQM 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)

TimeSpeakerTalk
9.00 amSimon BoothroydWhich 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 amDavid HahnParsley 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)

TimeSpeakerTalk
8.30 amMichael GilsonHow many Lennard-Jones atom types does a force field need?
Results of a data-driven investigation.
YouTube | Zenodo (video + slides)
9.00 amJeffry SetiadiHost-guest binding calculations with OpenFF Evaluator
Current status of pAPRika integration with OpenFF Evaluator.
YouTube | Zenodo (video + slides)

Day 5 (May 1, 2020)

TimeSpeakerTalk
8.30 amOwen MadinFuture 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 amYuanqing WangNear-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 amHyesu JangUpdate 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.

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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)

Discussion notes for Day 1

TimeEventSpeaker
7.30 - 8.15_ Breakfast _
8.15 - 8.30WelcomeOpenFF PIs
8.30 - 9.15Progress and status for the OpenFF small molecule force fieldVideo
9.15 - 10.00OFF Toolkit Showcase: Current capabilitiesVideo
10.00 - 10.30Discussion of progress and current statusVideo
10.30 - 11.00_ Coffee break _
11.00 - 11.30Parameterization perspective I: Parameterization methodologyVideo
11.30 - 12.00Parameterization perspective II: Property CalculatorVideo
12.00 - 12.15Parameterization perspective III: Data for parameterization and validation - QCArchiveVideo
12.15 - 12.30Parameterization perspective IV: Data for parameterization and validation - Physical propertiesVideo
12.30 - 13.30_ Lunch _
13.30 - 14.30Open discussion of the morning talks: Feedback and outlook for Y2, near-term planning, challengesChair: Mike Gilson
14.30 - 15.15Breakout session I: Force field assessment - physical properties of small moleculesChair: Michael Shirts
14.30 - 15.15Breakout session I: Chemical perception / addition of new parameters / chemical space coverageChair: David Mobley
15.15 - 15.30Breakout session reports
15.30 - 16.00_ Coffee break _
16.00 - 16.45Breakout session II: Force field assessment - protein-ligand free energies - [discussion summary]Chair: John Chodera
16.45 - 17.00Breakout session II: Parameter definition, dataset selection, optimization strategiesChair: Lee-Ping Wang
18.30**_Workshop dinner:_** ** Rock Bottom Brewery**


Day 2 (Aug 31)

Discussion notes for Day 2

TimeEventSpeaker
7.45 - 8.30_ Breakfast _
8.30 - 9.30Advisory Board meeting (closed)
9.30 - 10.15Future parameterization perspective: Plan for Year 2 and beyondVideo
10.15 - 10.45_ Coffee break _
10.45 - 11.30ANI-1 and neural net potentialsVideo
11.30 - 12.30Open discussion: Anticipated next force field development stepsVideo
12.30 - 13.00Concluding remarks and future outlook
13.00 - 14.00_ Lunch _
14.00 - 15.15Free discussion: Short-term and long-term plans for OpenFFConcurrent 1:1 sessions for Partners with J. Wagner
15.15 - 15.45_ Coffee break _
15.45 - 17.00Free discussion: ML perspectives in OpenFFConcurrent 1:1 sessions for Partners with J. Wagner


Day 3 (Sep 1)

Internal OpenFF team discussions and planning session.

TimeEventModerator
8.30 - 9.00_ Breakfast _
9.00 - 10.30Internal organization and project structureKarmen Condic-Jurkic
10.30 - 11.00_ Coffee break _
11.00 - 13.00Roadmap planning and deliverables for Year 2Karmen Condic-Jurkic
13.00 - 14.00_ Lunch _
14.00 - 15.00Summary
15.00 - 17.00Free 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.

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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

TimeEventSpeakerSlack channel
7.45 - 8.00Introduction [PDF] [Video]Gilson
8.00 - 8.30Roadmap overview [DOI] [Video]Shirts#project-planning
8.30 - 9.30Short-term parameter optimization strategy: ForceBalance [DOI] [Video]Wang#forcebalance
9.30 - 10.00Coffee break
#random
10.00 - 11.00Long-term parameter optimization strategy: Bayesian Fitting [DOI] [Video]Chodera#bayesian-inference
11.00 - 12.00Chemical perception and SMIRNOFF typing [DOI] [Video]Mobley/Bannan#smirnoff
12.00 - 1.00Torsion fitting and fragmentation [DOI] [Video]Chodera/Wang#torsions
1.00 - 2.00Lunch (catered)
2.00 - 2.30Group 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 ||

TimeEventSpeakerSlack channel
2.30 - 3.00Breakout Session 1
3.00 - 3.30Coffee break
#random
3.30 - 4.00Breakout Session 2
4.00 - 5.00Reconvene 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] |

TimeEventSpeakerSlack channel
5.00 - 5.15Roadmap recap and discussion (reviewing Slack input from remote attendees)
#project-planning
6.00Group dinner in La Jolla at Rock Bottom Brewing


Jan 8

Research topics 45 min talk + 15 min discussion

TimeEventSpeakerSlack channel
8.00 - 9.00Charge models [DOI] [Video]Schauperl#charge-models
9.00 - 10.00Fitting non-torsion valence terms [DOI] [Video]Mobley/Wang#valence
10.00 - 10.30Coffee break
#random
10.30 - 11.30Software architecture and infrastructure [DOI] [Video]Wagner#infrastructure
11.30 - 12.30Fitting condensed-phase properties [DOI] [Video]Chodera/Shirts#propertycalculator
12.30 - 1.30Lunch (catered)
1.30 - 2.00Group discussion to define ad hoc breakouts and breakout leaders/note-takers

Proposed Breakout Sessions: electrostatics, software preview / toolkit hands-on ||

TimeEventSpeakerSlack channel
2.00 - 4.00Breakout Session (with coffee)
4.00 - 5.00Reconvene and wrap-up discussion

Breakout session notes: neural network potentials [PDF] |