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openforcefield / standards

A repository of the standards employed across the Open Force Field Consortium.
https://openforcefield.github.io/standards
MIT License
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OFF-EP 0003 #23

Closed mattwthompson closed 5 months ago

mattwthompson commented 2 years ago

Resolves #8

SimonBoothroyd commented 2 years ago

This is a bit more of a tricky one as it goes against the current philosophy that all attribute names in the spec can mapped into code, so while length_bondorder1 is valid python (/ C / javascript...), length_bondorder1.5 won't be and so cannot be directly accessed.

@j-wags will probably have more thoughts on this though.

mattwthompson commented 2 years ago

Thanks for all the feedback - I think this is heading in the right direction but it'll take a bit more care to get it into a state that is ready for another review. In particular, this idea won't immediately work so cleanly for torsions - mostly because the current kN_bondorderM approach squeezes the periodicity and bond order together in a way that could be confusing. Maybe kN_M is fine, I'll don't want to decide now.

jchodera commented 2 years ago

In particular, this idea won't immediately work so cleanly for torsions - mostly because the current kN_bondorderM approach squeezes the periodicity and bond order together in a way that could be confusing. Maybe kN_M is fine, I'll don't want to decide now.

I don't understand this. What is kN_bondorderM and kN_M?

mattwthompson commented 2 years ago

For interpolated (periodic) torsions, there are different force constants for each periodicity and interpolation point. Like in the

<ProperTorsions ... >
    <Proper ... k1_bondorder1="1.00*kilocalories_per_mole" k1_bondorder2="1.80*kilocalories_per_mole" idivf1="1.0"/>
    ...

It's a matter of picking the best variable name for encoding this. Above you suggested k_bondorder2 -> k2 for bonds, which doesn't work 1:1 as in torsions (k1_bondorder2 -> k1_2 would be confusing and somewhat ambiguous). k1_bondorder is probably better.

mattwthompson commented 5 months ago

This doesn't seem to be so important after all, but it's all laid out here if somebody wants to do it