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End goal - A one time artifact (possibly blog post, optionally with a repo) stating whether Interchange can get various ecosystem tutorials to get identical energy evaluations in OpenMM, and documenting the severity/details of disagreement if not.
Week Part 1
: Select condensed phase system setup tutorials (AMBER+GROMACS+ optionally others)Status colour YellowGreen title in progressComplete Ideally 5+ (it’s fine if there are many simple ones)
Exclude tutorials that need more than conda-installable deps
Aim for a diversity of inputs (small mols, protein, nucleic acids, lipids)
Optionally, include a collection of “won’t even bother” tutorials (vsites, metals, alternative nonbonded)
Goal: Present the tutorials selected and what kinds of coverage they add to study
Week Part 2
: Select a specific MD config, parameter, and coordinate file from each tutorial.Status colour Yellow title not startedin progress The files selected don’t need to be the minimized/post-simulation coordinates, but they should include all chemical components in the final system.
Filter out ones that don’t work at all
Optionally, if components from tutorial are output separately, try combining them using `+` operator
Goal: Present the run config, parameter, and coordinate files to be used for each tutorial, documenting any decisions made or deviations from the tutorial to get them.
Week Part 3
: Evaluate energies for each tutorial’s files natively and in OpenMM via InterchangeStatus title not started Run in both the native engine and OpenMM, comparing energy components.
Optionally, fix “low-hanging fruit”
Optionally, do also convert from native to OpenMM using ParmEd
Goal: Present a table of energy values (native vs. OpenMM-via-Interchange) for the systems selected from each tutorial, ideally broken down by component
Week Part 4
: Write up one-time study/blog postStatus title not started Add Zenodo DOI in some form
Goal: A website PR adding a blog post presenting the above table and explaining how the study was run.
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