MolSSI Community Highlight: Dr. Jeffrey Wagner, Open Force Field Consortium
MolSSI Community Highlights spotlight exceptional examples of research and education enabled by MolSSI software and educational resources.
Dr. Jeffrey Wagner (Technical lead at the Open Force Field Consortium) and his team focus on the development of accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. In this post, Dr. Wagner tells us how MolSSI tools have played a role in advancing the development and validation of molecular forcefields.
MolSSI:
Hi Dr. Wagner, thank you for taking the time to chat with us! Your research area seems fascinating. Could you provide a brief introduction to your research area and share what your team is currently focusing on?
Dr. Wagner:
The Open Force Field Consortium (OpenFF) is a collaboration of academic and industrial researchers that aims to develop accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. The consortium’s ultimate goal is to enable more accurate computational simulations of molecular systems in a variety of fields, including drug discovery and materials science.
To achieve this goal, we use a variety of computational and experimental techniques, including QM calculations, molecular dynamics simulations, and machine learning methods, to generate and validate force field parameters. We also work to develop best practices and standards for force field development, validation, and sharing.
MolSSI:
Can you share how MolSSI software tools or resources have been utilized to accomplish specific research objectives in your projects?
Dr. Wagner:
The Open Force Field Consortium (OpenFF) heavily relies on the MolSSI software tools and resources to achieve specific research goals. The Parsley and Sage force field lines, which are used in many of our research projects, were developed based on quantum chemical data calculated on the MolSSI QCArchive. This data serves as a reference to validate and improve our force fields. Furthermore, the OpenFF QCSubmit package and qca-dataset-submission pipeline interface with the MolSSI APIs to allow us to easily create cross-ecosystem workflows, making it possible to use the MolSSI ecosystem tools to fit and validate force fields that interact with the OpenMM and other toolkits. Many of our lead employees were trained in software development at MolSSI, which has greatly contributed to the development of the OpenFF toolkits.
We also make heavy use of the MolSSI QCArchive and general QC ecosystem to generate and share quantum chemical datasets for force field fitting. This includes using the QCSubmit package to automatically submit calculations to the QCArchive for small molecule and protein systems. The QCArchive provides us with access to a large database of computed molecular properties, which allows us to validate and benchmark our force fields against accurate reference data. In addition, many of our repositories, including the OpenFF toolkit, are based on the MolSSI project cookiecutter. Overall, the collaboration between OpenFF and MolSSI has been instrumental in our research endeavors, allowing us to develop more accurate and transferable force fields and to improve the accessibility and sharing of quantum chemical datasets.
MolSSI:
It’s great to see the impact of MolSSI resources on your work. Could you please share some of your significant findings or results facilitated by the MolSSI software tools or resources?
Dr. Wagner:
We have published several papers incorporating MolSSI software tools and resources, including the development and benchmarking of the Parsley and Sage small molecule force fields.
MolSSI
MolSSI greatly values our collaboration with the Open Force Field Consortium. We extend our thanks to Dr. Wagner for sharing his insights with our community. We’re excited to continue supporting their important work in developing accurate molecular mechanics force fields.
Here are some publications that incorporate MolSSI software tools or resources from The Open Force Field Consortium:
- Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field: https://doi.org/10.26434/chemrxiv-2022-n2z1c
- Collaborative assessment of molecular geometries and energies from the Open Force Field: https://doi.org/10.1021/acs.jcim.2c01185
- Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale: https://doi.org/10.1021/acs.jcim.2c01153
- Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field https://doi.org/10.1021/acs.jctc.1c00571
- End-to-end differentiable construction of molecular mechanics force field https://doi.org/10.1039/D2SC02739A
- Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans https://doi.org/10.1101/2020.08.27.270934
- Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields https://doi.org/10.12688/f1000research.27141.1
- Driving torsion scans with wavefront propagation https://doi.org/10.1063/5.0009232
All of the Parsley and Sage force fields here: https://zenodo.org/record/7889050