Page Comparison

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.

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.