02-09-22 Interchange Check-in

Goal: calculation interaction energy between two molecules

• HJ Issue: Allowed to have no box?

  • MT: In general, it should be allowed and set or not set based on the input topology, but some exports might be buggy.

  • MT will raise issue and make bugfix patch

• HJ issue:

• Lack of from_amber. So I tried from_gromacs to generate the same interchange file.

MT – For the second row, this is probably a bug. I’ll raise an issue. I’m not sure which version we have you using, this may be fixed more recently now that the toolkit has residue info.

HJ – Rows after that complain because molecule names have spaces, or there’s like a field overflow

HJ – When writing to- and then reading files from gromacs format, I get the mixing rule error.

• MT – Thanks. That’s a bug. That should be an easy fix.

HJ will share notebook that exercises bugs discussed here

MT will notify HJ when bugs are fixed, provide update/install instructions

JW – Are there cases where we don’t plan to support roundtripping? Like, Interchange → GROMACS –> interchange will not, in general, yield an identical Interchange object (since the info content of a GMX file isn’t the same as the info content of an Interchange)

• MT – I don’t think we have any PROscriptive rules about that. We want to support as many roundtirps as are reasonable, but some of them won’t be possible due to information content issues.

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JW – Openeye undefined behavior for residue getting/setting

JW will send HJ reproducing example of undefined value returns for unset hierarchy info from OE toolkit.