Open Force Field
- Reposted by Open Force FieldNot one but 2 (!) open #postdocjobs to work with me 1️⃣ tinyurl.com/EPSRCMattaPDRA 2-year postdoc on data-driven design and screening of organic mixed conducting materials ⚡️🔋 #omiecs Deadline: Feb 8 Ideal profile: MD or DFT skills, experience in #high-throughput workflows, strong coding skills
- #documentation makes the difference between a piece of code and a tool. @omsf.io is developing deep expertise in documenting #opensource scientific software, and now shares this expertise in a "playbook," including contributions from our own Josh Mitchell. playbooks.omsf.io/documentation/
- We’re pleased to announce the full release of the Sage 2.3.0 force field! This is identical to the previous release candidate Sage 2.3.0rc2. Sage 2.3.0 is the first OpenFF force field to use the AshGC neural network charge model. github.com/openforcefie... #compchem
- Sage 2.3.0 maintains or improves performance on all of our benchmarks except solvation free energies in nonaqueous solvents. Please try it out and let us know if you find any substantial improvements, regressions, or other issues in comparison to Sage 2.2.1!
- New preprint describing our GNN charge model, AshGC! Since QM methods of charge assignment scale poorly to larger molecules, and are also conformation dependent, AshGC leads to major performance improvements in this critical step in force field parameterization. chemrxiv.org/engage/chemr...
- These results are also a benchmark of our force field, Sage 2.2.0!
- OpenFE is ready for production! chemrxiv.org/engage/chemr... In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets. #compchem
- The Open Force Field Consortium welcomes two new members to our Governing Board: Daniel Cole (of @colegroupncl.bsky.social ) and Thomas Steinbrecher (of Roche)!
- To showcase the unique capabilities of our upcoming force field, OpenFF 3.0 “Rosemary,” we've released an improved version of our PTM prototype workflow for parameterizing a protein with post-translational modifications. github.com/openforcefie...
- Jeff Wagner and Jen Clark ran a workshop at the @mdanalysis.bsky.social UGM in Arizona last week, in coordination with the @openfree.energy team.
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- Chapin Cavendar's paper, Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields, is out now in LiveCoMS. Read it for a detailed look at the great work he has been doing toward an OpenFF protein force field, and stay tuned! livecomsjournal.org/index.php/li...
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- AshGC v1.0 is our first neural network charge model. It has been trained to produce charges that are comparable to OpenEye AM1-BCC-ELF10. AshGC 1.0 is identical to the previously released AshGC rc3, except it adds support for single-atom charges. docs.openforcefield.org/projects/nag...
- We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
- Please try it out and let us know if you find any substantial improvements, regressions, or other issues in comparison to Sage 2.2.1. If all goes well, we plan to make the full release in a few weeks! See the thread for an example:
- OpenFF provides a critical resource for pharmaceutical discovery and design, producing high quality force fields that can be applied at scale without commercial license fees. Learn how your company can partner with us to invest in the future of #openscience app.reclaim.ai/m/james-omsf...
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- Hot take from our Project Director, David Mobley: We should drop bond order and no longer use aromaticity. blog.omsf.io/why-we-shoul... Do you agree, #chemsky ?
- We're excited to see this work from @micaelamatta.bsky.social and @hannahturney.bsky.social in publication! They have done some really cool work with our toolkit, and pushed us to to make several performance enhancements for loading and parameterizing polymers.
- Our toolkit is designed to meet the needs of force field scientists -- that's who we are! Here's an example of how easy it is to change parameters in a force field in our format: docs.openforcefield.org/en/latest/ex... #opensource #compchem
- It's great to see others using NAGL to train GNN charge models. Stay tuned for our own model, coming soon!
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@jenkescheen.bsky.social showcased his work on @asapdiscovery.bsky.social and more recently with CharmTx, combining ML and more traditional free energy calculations. A lot, if not all, of his work is based on @openfree.energy, #openforcefield, and #alchemsicale. Read his papers for more details! - This tool has solved some of our CI problems. #opensource #devops
- Maybe all you want to do is prepare your "ligand" (which isn't a ligand at all if it's not binding to a protein, but let's imagine it will one day) in a box of water and equilibrate the system. We have an example for that! docs.openforcefield.org/en/latest/ex...
- If you're looking for updates on the latest scientific progress at Open Force Field, look no further! youtu.be/kvThLGXnUrU #opensource #openscience #compchem
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- Reposted by Open Force FieldThe Free Energy Workshop (feworkshop.bsky.social) will happen on May 6-8th. If you're an unemployed #CompChem modeller or researcher and want to attend to network but cannot afford the $215 registration fee, please DM me.
- Our infrastructure lead, Jeffrey Wagner, prepares monthly updates on the progress of the infrastructure team. They're available on Youtube once a month on Tuesdays. youtu.be/7llP6SULP-M?... #opensource #compchem
- If you want to use our force field with a wide range of MD engines, you want to use Interchange. Here's an example of setting up a protein-ligand-water system and then exporting to OpenMM, Amber, LAMMPS, and GROMACS: docs.openforcefield.org/en/latest/ex... #opensource #compchem
