Open Force Field Consortium Virtual Meeting

The Third Open Force Field Consortium Workshop in Zoomverse on May 4-5, 2020.

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We are hosting the Third Open Force Field Consortium Workshop, this time in the online world of Zoom, on May 4-5, 2020. This virtual meeting is replacing the planned in-person gathering in Boston. We decided to slightly experiment with the workshop format by making most of the content available before the meeting for asynchronous consumption. Namely, all talks will be pre-recorded and the meeting time will be focused on discussions around those talks and future planning. TDavid Cerutti, who has recently joined the Open Force Field Initiative as a senior scientist and who will lead the NIH-funded efforts in the biopolymer arena, will give a virtual keynote and a brief summary of his talk before discussion. The main aim of this format is to make this virtual meeting more interactive, and hopefully, more productive.

Talks and discussions

The meeting attendees can join the recording sessions, if they wish, or watch the videos later at their own convenience. Each talk will be 15 min long and there will be 15 min for questions and comments. Read in the Zoom policy below how to join the meetings.

The talks will be uploaded to our YouTube channel on the day when they are recorded. The recording session schedule is provided below and the YouTube links and slides will be shared as soon as the videos have been uploaded. To access presentation slides and better video quality, download provided content from Zenodo.

Discussion session schedule is in preparation and it will be posted soon, but one of the planned discussions will be focused on user experience. To help us understand better your needs and your use cases, please respond to this survey.

Zoom policy

The schedule for recording sessions and discussions will be available on the website, however, the Zoom links and passwords will be shared via email with all registered participants. This is a precautionary measure to reduce the probability of Zoom bombing. If any of your colleagues or collaborators would like to join the meeting, please ask them to register here with their institutional email account. All Zoom meetings have the waiting room enabled.

Registration

The meeting is primarily intended for the members of the Open Force Field Consortium and Initiative, but all talks and some parts of the meeting are open to the interested members of the community. Please register with your institutional email using the form below (if you use your personal email account you may risk not receiving meeting details). Please note that some discussions might not be open to general public.

Details at a glance

  • Recording sessions: Every day from Apr 27, 2020 (Monday) to May 1, 2020 (Friday) between 8.30-9 am (Pacific Time).

  • Discussion sessions: May 4-5, 2020 between 8 am - 12 pm (Pacific Time).

  • Organiser: Karmen Condic-Jurkic <info@openforcefield.org>

  • Registration form: https://forms.gle/aw3jTnAaKzMuBspBA


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

Time Discussion
7.00 am Session I: Current status and performance of Open Force Fields and infrastructure
- David Mobley: A brief recap from talks and introduction (10-15 min)
- 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
10.00 am Wrap-up discussion

Day 2 (May 5, 2020)

Meeting notes - Day 2

Time Discussion
7.00 am Session I: Biopolymer force fields
- Michael Shirts: Aims for the NIH-funded biopolymer force fields (15 min)
- David Cerutti: Strategies for ab initio Biomolecular Force Field Development (15 min)
YouTube | Zenodo
- Discussion (45 min)
8.30 am Break
8.45 am Session II: Future directions
- Bayesian framework
- Machine learning applications

Relevant talks (by theme): Future Directions
10.00 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 Training dataset selection

QM data selection for openff-1.2. 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

The calculated binding free energy results between proteins and Parsley-parameterized ligands will be discussed. Alongside, the infrastructure for protein ligand benchmarking is presented.
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, 1.2.0)

Valence parameter re-fitting was done with (1) parameter definition adjustments and (2) newly designed QM training set and the validation of improved performance was carried out.
YouTube | Zenodo (video + slides)

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