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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

    Status
    colourYellowGreen
    titlein progressComplete
    : Select condensed phase system setup tutorials (AMBER+GROMACS+ optionally others)

    • 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

    Status
    colourYellow
    titlenot startedin progress
    : Select a specific MD config, parameter, and coordinate file from each tutorial.

    • 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

    Status
    titlenot started
    : Evaluate energies for each tutorial’s files natively and in OpenMM via Interchange

    • 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

    Status
    titlenot started
    : Write up one-time study/blog post

    • 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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