OpenFF Science Roadmap 2020

This scientific roadmap includes the next two planned force field releases and a list of scientific studies which need to be performed in 2020. Each study has a priority assigned to it. This roadmap will be continuously updated.

Force Fields

Upcoming force field versions:

Version

Codename

Features

Expected release date

Comment / Blocker

Version

Codename

Features

Expected release date

Comment / Blocker

openff-1.2.0

Parsley

  • Redesigned QM dataset for parameterization with better/broader coverage

  • Parameter fixes

Expected: May 2020

Released: Jun 3, 2020

 

openff-1.3.0

Parsley

When ready. September-December 2020.

 

openff-2.0.0

Sage

  • LJ refit (based on the ongoing feasibility study)

  • Limited WBO torsion interpolation for systems for which data already exists (more torsional data needed for a wide range application)

Exepected: Release date to be set by November 2020 and will have three month lead time. Likely release between December 2020 and Feb. 2021.

  • How fast can we do WBO interpolations (Pavan)

  • @Simon Boothroyd needs to get in touch with @David Hahn and folks from the Chodera lab to discuss some free energy benchmarking after LJ fitting

  • Late 2020/early 2021 still feasible

Scientific studies

The list of scientific studies which need to be performed in 2020, which will be updated every 3 months, as suggested in the science project management workflow. Each study should be linked to its Confluence page with more information about study design, execution and results. The study design should be submitted before study is about to begin.

Estimate start dates and end dates when possible before study has started. Record the real start and end dates for each study below the estimated dates.

Labels

Category

Labels

Category

Labels

Priority

high | MEDIUM | LOW

Effort

high | MEDIUM | LOW

Status

Not started | In Progress | PROTOTYPE | Completed | BLOCKED |

 

Study

Priority

Effort

Science dependencies

Infrastructure dependencies

Comment

Start date

End date

Status

Driver/Team

Chemical perception

Addition of new parameters – manually fixing problems

 

high

high

 

Made easier by benchmarking dashboard (Optional)

Made easier by benchmarking dashboard (Optional

 

 

in progress

@Hyesu Jang @David Mobley @Jessica Maat @Victoria Lim (Deactivated)

Automated typing inference from scratch

Medium

high

 

 

Organise a meeting to coordinate efforts.

Update: @Tobias Huefner is doing some basic research, but we don’t have a timeline defined here. Perhaps a more specific study to look at typing issues similar to Schauperl’s work on LJ typing.

 

 

in progressSlowly

Full-time person needed – to be discussed further. Work of @Josh Fass (Unlicensed) and @Tobias Huefner may assist here. @Owen Madin interested. @Trevor Gokey is also actively working in this area.

Mixture Properties

https://openforcefield.atlassian.net/wiki/spaces/FF/pages/122454022/Binary+Mixture+Data+Feasibility+Study

high

 

 

 

In the writing stage.

 

 

COMPLETED

Driver: @Simon Boothroyd
Team: @Michael Shirts @Owen Madin

https://openforcefield.atlassian.net/wiki/spaces/FF/pages/74055857/Non-bonded+optimization

high

high

 

 

Parent study for in a long-term progress stage.

 

 

in progress

Driver:@Simon Boothroyd
Team: @Michael Shirts @Owen Madin

Chemical potential-like properties

MEdium

 

Non-bonded optimization

Implementation in Evaluator

Need to evaluate the data first (testing needed). Add Confluence page here.

 

 

In Progress

PROTOTYPE

@Simon Boothroyd

spinoff

Solvent-solvent partition coefficients

MEdium

 

 

Implementation in Evaluator

  • Data needed, harder problem.

  • Update: Access to solubility phase, data is less of a problem now (MNSOL)

 

 

not started

@Simon Boothroyd spinoff

Data coverage and availability

high

 

Feasibility studies

 

Check the available data and identify missing data points. Worry in the future what to do about it. We will use what we have for Sage.

 

 

Ongoing

@Simon Boothroyd @Owen Madin @Michael Shirts

QM Data Generation

https://openforcefield.atlassian.net/wiki/spaces/FF/pages/146997319/QM+dataset+selection (training data) for OpenFF-1.2.0

high

 

 

 

Need to expand to benchmarking set.

 

 

completed

@David Mobley @Jessica Maat @Hyesu Jang

QM dataset selection for OpenFF-2.0.0

high

 

 

 

 

 

 

in progress

@David Mobley @Jessica Maat @Hyesu Jang
Lead: @Hyesu Jang ??

Benchmarking/re-evaluating our choice of QM theory

high

 

 

(Optional) QC Dataset submission infrastructure

Test of the whole torsiondrive. Keep within 10-50 torsiondrives. More is better.

  • Some datasets ready, but analysis is still required (@Hyesu Jang ) Pavan might help with this.

  • No changes made to our fitting data til after 2.0 release, but decision may be made before that (eg while fitting)

 

 

in progress

@Hyesu Jang lead; @Lee-Ping Wang @Pavan Behara

@Hyesu Jang also leading molecule set selection with help from @Jessica Maat and @Victoria Lim (Deactivated)

Protomer/tautomer enumerated molecules

high

 

QM level of theory validation (QMLoTV)

Protonation/tautomer enumeration integration (@Joshua Horton doing OE version in toolkit; there’s currently no good protonation state enumeration with RDKit – see )

  • It can only do enumeration with OpenEye

 

 

PRototyped

@Joshua Horton

Data selection for ionic species

 

 

 

 

What kind of experimental data would we need to include charged molecules?

 

 

NOt started

Lead: @Simon Boothroyd (oversight, to assemble team?)

Data on molecules with nonzero formal charges

high

 

QM level of theory validation (QMLoTV)

(Optional) QC Dataset submission infrastructure

Couples to benchmarking

 

 

NOt started

@Pavan Behara

Enamine REAL fragment coverage

MEDIUM

 

 

Automated fragmentation integration @Joshua Horton

 

 

 

in progress

@Trevor Gokey

Ligand Expo fragment coverage

MEDIUM

 

 

Automated fragmentation integration @Joshua Horton

Ligand Expo has higher priority than Enamine Real.

 

 

NOT started

 

Richer torsion data for WBO fitting

Low

 

 

WBO torsion implementation

  • What data to generate and

 

 

 

(person needed to continue work of @Chaya Stern (Deactivated); Will be @Pavan Behara with @Jessica Maat , eventually coordinating with @Simon Boothroyd as he moves to his new position. )

Biopolymer data selection (ensure sidechain data is available in QCA)

high

 

 

 

One dataset ready, but a lot more data needs to be generated if we want sidechain sampling

 

 

in progress

@David Cerutti (Unlicensed)

Biopolymer data computation

MEDIUM

 

 

(Optional) QC Dataset submission infrastructure

 

 

 

in progress

@David Cerutti (Unlicensed) @David Dotson

More efficient torsion sampling with less grid points during scan

Low

 

 

 

 

 

 

 

spinoff

Fitting

Addition of new parameters – manually fixing problems

high

high

 

 

 

Ongoing

 

in progress

@Hyesu Jang @David Mobley @Jessica Maat @Victoria Lim (Deactivated)

LJ refitting (Sage)

high

 

https://openforcefield.atlassian.net/wiki/spaces/FF/pages/74055857/Non-bonded+optimization

 

 

 

 

in progress

@Simon Boothroyd and @Owen Madin

WBO refitting (Sage)

high

 

More torsion data

WBO torsion implementation: Done.

Implement what Chaya has already done. Infrastructure ready.

@Pavan Behara and @Jessica Maat to divide up chemical space for fitting/test fixes. @Hyesu Jang will do central fitting of production FF. Additional discussion: https://openforcefield.atlassian.net/wiki/spaces/OFFO/pages/670629936/90-day+plan+Onboarding+for+Pavan+Behara?accessType=view&grantAccess=true&username=5f592e4d0b6be2006ef56679&userFullName=Pavan%20Behara#Notes-from-9%2F16%2F20-planning-meeting-(feel-free-to-migrate)

After May meeting

Late 2020 (Sep 2020)

in progress

@Jessica Maat and @Pavan Behara . @Pavan Behara will eventually oversee.

BCC refitting

high

 

LJ refit

Patterns for BCCs; could start with something simple like bond SMARTS.

ChargeIncrementModel implementation (early May)

 

 

 

in progress

@Simon Boothroyd @Owen Madin

Study how to set prior widths and weights for different sorts of data during FF optimization

medium

 

 

 

Became higher priority due to need for fixes. Headed towards a 1.3 release late 2020.

 

 

in progress

@Lee-Ping Wang @Hyesu Jang Spinoff?

Value of data generated “incidentally” during torsiondrive in fitting, e.g. optimization snapshots, gradients, energies (low control over these data points)

Low

 

 

Some parts of https://openforcefield.atlassian.net/wiki/spaces/IN/pages/62324892/Bespoke+workflow

  • Once we have more people working on fitting, someone can run this study

 

 

 

@Joshua Horton spinoff

Benchmarking

Small reference system for fast testing of FE infrastructure – 5-10 small reference systems, possibly subset of SAMPL challenges, for comparison of different free energy methods to avoid using large P-L systems for test calculations

Low

Low

 

 

Should use SAMPLing challenge systems plus a couple more similar ones.

 

ASAP

Not started

 

Benchmarking/re-evaluating our choice of QM theory

high

medium

 

 

See above; to be done while fitting 2.0 (datasets ready). @Hyesu Jang leading.

 

 

Not started

@Lee-Ping Wang @Hyesu Jang @Pavan Behara

CCDC data selection/release

Low

 

 

 

 

 

 

 

spinoff

Create a list of tests to judge the “quality” of biopolymer FF with our scientific advisory board

HIGH

 

 

 

Organise the meeting with our IAB, invite to May meeting. Done.

DC and MS will start conversations to get this going.

 

April / May

in progress

@David Cerutti (Unlicensed) @Michael Shirts

openff-1.2.0 (Parsley) benchmarking

 

 

Minor release of Parsley

Benchmarking dashboard

Done in preprint form, but no benchmarking dashboard. Still need torsion benchmarking; utilize work just done for OpenFF 1.0 paper.

JDC is trying to get a complete FE set run by D. Rufa.

 

Mid 2020

Done-ish

 

openff-2.0.0 (Sage) benchmarking

 

 

Release of Sage

Benchmarking dashboard

 

 

Late 2020

Not started

 

Biopolymers

Which quantum method should we use for biopolymers (should it be the same as small molecules)?

medium

 

QM benchmarking study

 

Short term – using the same method and same level of theory as ANI (wB97D)

 

 

Not started

@Lee-Ping Wang @David Cerutti (Unlicensed)

Feasibility/benchmarking studies of torsional CMAPs

medium

 

After protein FF implementation

CMAP support in OFFTK

 

 

 

Not started

@David Cerutti (Unlicensed)

Feasibility/benchmarking studies of other cross-terms

Low

 

 

Support for cross-terms in OFFTK

MS – Importance of cross-terms will be related to a number of types

 

 

Not started

 

Charges

GCN charge model

high

 

 

 

In a few steps:

  • conda-installable tool to assign charges

  • integration of tool into OFFTK under ChargeIncrementModel keyword (and exposure of relevant keywords)

 

 

in progress

@John Chodera @Yuanqing Wang (Deactivated) @Josh Fass (Unlicensed) (maybe John Herr)

Off-site charge SMIRKS definition/fitting/benchmarking

medium

high

 

VirtualSite support in OFFTK

Helpful discussion in Slack: https://openforcefieldgroup.slack.com/archives/C1907SGET/p1590251452068100

Infrastructure expected in September 2020

 

 

Not started

spinoff (but interface with @David Cerutti (Unlicensed) work?)

Bayesian inference and surrogate modeling

Testing Bayesian inference on an analytical model

medium

Low

 

 

Nearing completion

 

 

in progress

@Owen Madin

Generalizing analytical model for Bayesian inference and testing methods

LOW

medium

 

 

Proof-of-concept work to give us an analytical form for early testing

 

 

in progressslower

@Owen Madin (and a student)

Constructing full Bayesian architecture with reweighting and simulation to build surrogate models

LOW

high

Analytical Bayesian inference testing

 

ForceBalance → pytorch, torchMD (timemachine)

 

 

Not started

John Herr

@Owen Madin (science, not software)

Automated typing inference from scratch

high

high

 

 

Bayesian-based typing (Josh Fass’s work)

 

 

 

@Josh Fass (Unlicensed)@Tobias Huefner

Other

Water co-optimization planning study (to be executed later) – discuss with @Lee-Ping Wang

Low

high

 

 

Lack of bandwidth, potentially Bill Swope could help advise with data selection.

 

 

 

spinoff

Thinking about metals / ions / salts

Low

high

 

 

Biologically relevant, will become high priority at some point

 

 

 

spinoff

Thinking about ionic liquids

 

 

 

 

 

 

 

 

 

Alchemical force fields (for alchemical free energies)

Low/MEDIum

 

 

 

Soft core potentials. JDC might have people in his lab working on it, MS is interested to join the effort.

 

 

 

 

Continuous (smearnoff) typing

 

 

 

 

ESPALOMA

 

 

 

@Yuanqing Wang (Deactivated)