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mattwthompson avatar mattwthompson commented on July 22, 2024

Will look at this and your changes more closely later but you're probably running into the long-standing problem of using SMIRNOFF in "conventional" atom-typed infrastructure, namely the atom type explosion problem. It's the sort of problem that seems like it should be easy to wrangle but doesn't always work out like that - with some differences in how engines handle each. I forget (but hope I can pull up!) some of the more antagonistic cases that prevented me from going all the way with atom type de-duplication in the past.

This is all to say your issue is surely valid, I'm not surprised you're running into some performance issues, and I've even tagged this as something to better document (#607).

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pbuslaev avatar pbuslaev commented on July 22, 2024

Following the discussion in #606 the behaviour suggested in #962 can be made optional, by adding a flag to Interchange.to_gromacs(combine_atomtypes: bool = False). This will keep the possibility to write all possible atomtypes if needed, but will also give the users the possibility to reduce the memory load. This solution also does not put any constraintes on the core Interchange code, only to one particular exporter. This flag will also provide a direct way to test the functionality.

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