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 can be continuously updated, but the overall status and priorities will be revised and updated in June 2020.
Force Fields
Upcoming force field versions:
Version | Codename | Features | Expected release date | Comment / Blocker |
|---|---|---|---|---|
| Parsley |
| May 2020 / June 2020 | |
| Sage |
| Late 2020 (November) |
|
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 |
|---|---|
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 (Deactivated) 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 (Deactivated) and Tobias Huefner may assist here. Owen Madin interested. Trevor Gokey is also actively working in this area. | ||||
Mixture Properties | |||||||||
HIGH | In the writing stage. | COMPLETED | Driver: Simon Boothroyd | ||||||
HIGH | HIGH | Parent study for in a long-term progress stage. | IN PROGRESS | Driver:Simon Boothroyd | |||||
Chemical potential-like properties | MEDIUM | Non-bonded optimization | Implementation in | Need to evaluate the data first (testing needed). Add Confluence page here. | IN PROGRESS PROTOTYPE | SPINOFF | |||
Solvent-solvent partition coefficients | MEDIUM | Implementation in |
| 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 | |||||
QM Data Generation | |||||||||
QM dataset selection (training data) for OpenFF-1.2.0 | HIGH | Need to expand to benchmarking set. | COMPLETED | ||||||
QM dataset selection for OpenFF-2.0.0 | HIGH | IN PROGRESS | |||||||
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.
| IN PROGRESS | 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 | 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 ) |
| PROTOTYPED | ||||
Data selection for ionic species | What kind of experimental data would we need to include charged molecules? | NOT STARTED | |||||||
Data on molecules with nonzero formal charges | HIGH | QM level of theory validation (QMLoTV) | (Optional) QC Dataset submission infrastructure | NOT STARTED | Pavan | ||||
Enamine REAL fragment coverage | MEDIUM | Automated fragmentation integration Joshua Horton | IN PROGRESS | ||||||
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 |
| (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) | HIGH | One dataset ready, but a lot more data needs to be generated if we want sidechain sampling | IN PROGRESS | ||||||
Biopolymer data computation | MEDIUM | (Optional) QC Dataset submission infrastructure | IN PROGRESS | ||||||
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 (Deactivated) Victoria Lim (Deactivated) | ||||
LJ refitting (Sage) | HIGH | IN PROGRESS | |||||||
WBO refitting (Sage) | HIGH | More torsion data | WBO torsion implementation. Done. | Implement what Chaya has already done. As soon as infrastructure is ready. Done. | After May meeting | Late 2020 (Sep 2020) | IN PROGRESS | ||
BCC refitting | HIGH | LJ refit Patterns for BCCs; could start with something simple like bond SMARTS. | ChargeIncrementModel implementation (early May) | IN PROGRESS | |||||
Study how to set prior widths and weights for different sorts of data during FF optimization | LOW | 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 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 | 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 | NOT STARTED | ||||||
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 | |||||
| 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 | ||||
| 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 | |||||
Feasibility/benchmarking studies of torsional CMAPs | MEDIUM | After protein FF implementation | CMAP support in OFFTK | NOT STARTED | |||||
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:
| IN PROGRESS | John Chodera Yuanqing Wang Josh Fass (Deactivated) (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 (Deactivated) work?) | |||
Bayesian inference and surrogate modeling | |||||||||
Testing Bayesian inference on an analytical model | MEDIUM | LOW | Nearing completion | IN PROGRESS | |||||
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) | ||||||
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 | ||||||||
