General updates | JW – Thanks for reaching out to OE about packaging issue I’m preparing a live demo for the annual workshop. The plan is roughly to take a OpenFold output, add a ligand, (show off OpenFF stuff), and then pass it to OpenFE to do a bunch of free energy calcs. Are there any particularly cool interchange capabilities I should show off here? Interchange.minimize Interchange.visualize Export to GROMACS, AMBER, OpenMM + run? (take caution re system size → runtime) Serialize to/from json, emphasize implications for portability Interchange.combine? Interchange.from_openmm? Big picture: In-place ligand evolution example? MT – Seems possible on a technical level. Not sure how useful/accurate zero-point energy evals would be. If you just have a ligand in vacuum, the physics would be lickity split, but the repeated exports to OpenMM could be slow. The sketchiest part would be modifying ligand in place- Could be possible with advanced interchange stuff but we probably don’t want to show that publicly. JW – Would make a new interchange for each ligand MT – That makes sense, you should still be cautious with runtime. … JW – If you have any code handy to visualize a minimization trajectory, LMK.
OMMFFs - Thanks for guiding meeting. I’m pushing lead team to work with OpenFE+JC lab on long term plan. MT – PE merged my PR into OpenMM, haven’t manually tested yet. No word on release timeline. MT – OMMFFs repo has everything in that I wanted (lots of old PRs merged, including the change discussed from yesterday where GAFFTemplateGenerator raises an error). MH will tag the release today. Not sure about ETA for conda packages. MT – Not sure about package splitting plans (having a base package without ambertools). Advocating for packaging constraints being Py3.10-12 and AT22+23. MT – so that should handle us well. Things should be workable early next week. Then everything will get clean once the OpenMM PR is in a release. JW – My next step is to nudge PE to make a bugfix release of OpenMM. Anything you see that would indicate I shouldn’t do that? MT – Re: Long term planning - … JW – We basically want to feed all the information into JE+DM (costs, alternatives, feelings, etc) and have them make a call that binds OpenFF and OpenFE to a single coordinated course of action (possibly involving agreements with JC lab as well).
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