👀 Overview
Summary | One reason our protein force field candidates may not approach the performance of AMBER force fields may be because we are getting stuck in a nearby local minimum. Loosening torsion priors may help us move away from this minimum. Torsion priors have not yet been updated in this investigation so far. This is related to the different optimization algorithms approach. |
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GitHub repo/branch |
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Status | NOT STARTED IN PROGRESS COMPLETED WON'T PROGRESS |
\uD83D\uDEA9Â Milestones and metrics
Stage | Milestone/Benchmark | Contributors | Deadline | Status |
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Fit Sage from small molecule and protein data with looser torsion priors | Starting from an up-to-date version of the protein-param-fit FF ( ), run a re-fit with the same data but increasing the torsion priors to 10 kcal/mol (up from 5 in previous fits) | Dec 01 | IN PROGRESS | |
Check how much torsions changed in new and previous re-fits | Check parameter changes | |||
Small molecule benchmarks | Run small molecule QM benchmarks | PASSED FAILED | ||
Protein stability benchmarks | Run GB3 benchmarks. Can likely decide whether to progress based on performance over 5 us | Â | NOT STARTED | |
Helix folding benchmark | Run helix folding benchmark | Â | NOT STARTED | |
Smaller peptide benchmarks | Smaller peptide NMR scalar coupling benchmarks | Â | NOT STARTED |