Page Comparison

Study

Priority

Effort

Science dependencies

Infrastructure dependencies

Comment

Start date

End date

Status

Driver/Team

Chemical perception

Addition of new parameters – manually fixing problems

Made easier by benchmarking dashboard (Optional)

Made easier by benchmarking dashboard (Optional

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

Automated typing inference from scratch

Organise a meeting to coordinate efforts.

Full-time person needed – to be discussed further. Work of Josh Fass (Deactivated) and Tobias Huefner may assist here. Owen Madin interested.

Mixture Properties

Binary Mixture Data Feasibility Study

Driver: Simon Boothroyd
Team: Michael Shirts Owen Madin

Non-bonded optimization

Driver:Simon Boothroyd
Team: Michael Shirts Owen Madin

Chemical potential-like properties

Non-bonded optimization

Implementation in Evaluator

Need to evaluate the data first (testing needed)

Simon Boothroyd Spinoff (student)

Octanol-water partition coefficients

Implementation in Evaluator

Data needed, harder problem

Simon Boothroyd spinoff (Student)

Data coverage and availability

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

QM dataset selection (training data)

Need to expand to benchmarking set.

David Mobley Jessica Maat (Deactivated) Hyesu Jang

Benchmarking/re-evaluating our choice of QM theory

(Optional) QC Dataset submission infrastructure

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

Hyesu Jang lead; Lee-Ping Wang

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

Protomer/tautomer enumerated molecules

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

Data on molecules with nonzero formal charges

QM level of theory validation (QMLoTV)

(Optional) QC Dataset submission infrastructure

Enamine REAL fragment coverage

Automated fragmentation integration (Joshua Horton

Trevor Gokey

Ligand Expo fragment coverage

Automated fragmentation integration (Joshua Horton

Ligand Expo has higher priority than Enamine Real.

Richer torsion data for WBO fitting

WBO torsion implementation

(person needed to continue work of Chaya Stern (Deactivated); probably Pavan with input from Jessica Maat (Deactivated) or vise versa. Overseen by Simon Boothroyd ? )

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

ASAP

David Cerutti (Deactivated)

Biopolymer data computation

(Optional) QC Dataset submission infrastructure

David Cerutti (Deactivated) David Dotson

More efficient torsion sampling with less grid points during scan

Fitting

Addition of new parameters – manually fixing problems

Ongoing

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

LJ refitting (Sage)

Non-bonded optimization

Simon Boothroyd and Owen Madin

WBO refitting (Sage)

More torsion data

WBO torsion implementation

Implement what Chaya has already done. As soon as infrastructure is ready.

After May meeting

Late 2020 (Sep 2020)

Jessica Maat (Deactivated) Hyesu Jang Someone else to continue where Chaya left it off

BCC refitting

LJ refit

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

ChargeIncrementModel implementation (early May)

Person needed (

David Mobley can help

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

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)

Some parts of Bespoke workflow

Joshua Horton

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

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

ASAP

David Mobley Michael Gilson John Chodera David Hahn – owner

Benchmarking/re-evaluating our choice of QM theory

Lee-Ping Wang

CCDC data selection/release

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

Organise the meeting with our IAB, invite to May meeting

April / May

David Cerutti (Deactivated)

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.

Mid 2020

Done-ish

openff-2.0.0 (Sage) benchmarking

Release of Sage

Benchmarking dashboard

Late 2020

Biopolymers

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

QM benchmarking study

Lee-Ping Wang David Cerutti (Deactivated)

Feasibility/benchmarking studies of torsional CMAPs

After protein FF implementation

CMAP support in OFFTK

David Cerutti (Deactivated)

Feasibility/benchmarking studies of other cross-terms

Support for cross-terms in OFFTK

Charges

GCN charge model

In a few steps:

• conda-installable tool to assign charges

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

John Chodera Yuanqing Wang

Off-site charge SMIRKS definition/fitting/benchmarking

VirtualSite support in OFFTK

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

Bayesian inference and surrogate modeling

Testing Bayesian inference on an analytical model

Owen Madin

Generalizing analytical model for Bayesian inference and testing methods

We don’t need Bayesian framework to work immediately

Simon Boothroyd

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

Analytical Bayesian inference testing

Simon Boothroyd Owen Madin Matt Thompson ?

Automated typing inference from scratch

Full-time person needed – to be discussed further. Work of Josh Fass (Deactivated) and Tobias Wulsdorf may assist here.

Other

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

spinoff

Thinking about metals / ions / salts / ionic liquids

Owen Madin Matt Thompson spinoff