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2024-04-02 SMIRNOFF committee meeting note

2024-04-02 SMIRNOFF committee meeting note

Participants

  • @John Chodera

  • @Lily Wang

  • @Matt Thompson

  • @Jeffrey Wagner

Discussion topics

Item

 

Notes

Item

 

Notes

Scheduling

 

MT

  • JC: conflict will not be an issue in future

EP 10

 

LW/JC

  • Yutong Zhao just mentioned more numerically stable version

  • To do:

    • Change vector notation

    • mention there could be numerical stability issues around 0 and pi

    •  

  • JC – IJKL vs …

    • LW – I’m 99% sure that it doesn’t make a difference.

    • JC – So matching direction doesn’t make a difference. Other cases that are dangerous?

    • LW – Cases where torsion profile itself isn’t symmetric around 0

    • JC approved PR + left remaining to dos as comments

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PR #63

 

JW

  • JW + JC + LW – We should invite Tom to begin a formal spec change proposal, which we will likely approve.

    • DM – Agree

    • JW will write to tom to invite formal change proposal

  • JW – General framework for considering vsites other than brute-forcing all edge cases? Something like symmetry groups in inorganic chem (c2v etc?)

    • MT – I think SMIRNOFF vsites are a genuinely new question

    • LW – re the particular question in the EP regarding the instability for fitting (multiple vsites wiht 1 spec vs one type with multiple capabilities) I doubt there’s an xisting general solution for this

    • DM – I’m thinking more carefully about some things - eg the nitrogen planarity thing was another edge case. I don’t see a general solution. So we probably want to do relatively narrow expansions of the spec instead of trying to make things highly general (since then we’ll hit cases/geometries that nobody’s thought of yet).

  • JW – Re the restrictions on monovalent and divalentlonepairs, I’ll look into adidng a named argument to skip emitting an error if they’re applied to an unexpected valence.

    • DM – Ok

  • (discussion about how to apply multiple vsites to same parent atom)

    • (currently implementation does this using name field to decide collisions, DM suggests alternatively using a field like “group” where all members of a group could coexist on a parent atom but if a vsite from another group is added the previous group would be removed. DM thinks it’s more imporant to document the current behavior in the spec than to document a new behavior and also implement it)

    • MT – Big problem with current implementation is that the logicthat toolkit uses to decide whether vsites are different are a tuple of (type, orientation atoms, name) and the existing behavior may be “surprising” to scientists, even if it’s “correct”.

    • JW – Any objection to me starting the process to EP the vsites page from OFFTK?

      • DM + LW – Agree

      • MT – Might be good to do it in steps.

    • JW – Ok, I’ll start this.

    • .

General forum

 

Action items

Decisions