Obtain performance benchmarks of OpenFF forcefields via geometry optimizations of in-house molecules by industry partners.
Due date
Key outcomes
partners can deploy required software with minimal difficulty
partners can execute geometry optimizations for the desired list of forcefields on their in-house molecules using their own compute and storage infrastructure
geometry optimization results are readily usable to reproduce key figures from the recent benchmarking preprint by Lim et. al.
Status
Problem Statement
The Open Force Field Initiative’s industry partners are keen to benchmark the performance of the recent OpenFF forcefields on their in-house, proprietary molecules. To do so, they will require minimally-complex tooling to perform geometry optimizations on these molecules at reasonable scale (100 to 1000 molecules) using a variety of force fields. They will also require tooling to reproduce key figures from the Lim et. al. preprint for these data.
The results of these calculations will be compiled together for publication.
Scope
Must have:
Each partner should be able to run geometry optimizations on 100 to 1000 proprietary molecules, each with 10 conformers (1,000 - 10,000 optimizations total).
Molecules that partners are willing to make public will be submitted to the public QCArchive for hosting/compute
The approach cannot be dependent on the OpenEye Toolkit.
Each optimization should be identified by a three-letter company code (COM), molecule-index (XXXXX), conformer-index (YY): COM-XXXXX-YY
Optimizations should be readily usable to reproduce key figures from the Lim et. al. preprint.
The following QM computation specs will be used:
default
program: psi4
method: B3LYP-D3BJ
basis: DZVP
The following MM force fields shall be used for optimizations with OpenMM:
smirnoff99Frosst
openff 1.0.0 1.1.(0,1) 1.2.1 (latest), 1.3.0 (upcoming as of 2020.10.22)
gaff2.1
Results from calculations must be flat files
Nice to have:
Coverage reporting (how often each parameter used; fragments that could not be parameterized)
Check if this is a must have
Energy minimizations with Schrodinger using OPLS3e as a separate software path (cannot be done with QC* software stack
need to obtain consent from Schrodinger for publishing; perhaps a partner can negotiate on behalf of the effort?
Dipole moment-based comparison for optimized geometries
Torsional difference comparison for optimized geometries
Not in scope (for this project; of interest for future projects):
Possibility to run torsion drives
Bespoke parameterization for molecules that can’t be parameterized by existing OpenFF forcefield, followed by benchmarking (requires injection of new parameters into QC* stack; not currently possible)
Benchmarking with MMFF94 and/or cGenFF
Clarifications Needed
What will the input file formats be? Will we enforce 3D SDF for minimal ambiguity?
Yes, enforce 3D SDF to remove possibility for ambiguity in inputs
Plot out milestones and deadlines using the table below. Put each milestone on its own row, @mention milestone owners, and type /date to quickly add deadlines.
Milestone
Owner
Deadline/Date
Status
Meeting with industry partners; gather comprehensive requirements/desires
