openff-interchange

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Improve Amber parsers

1

### Description Provide a brief description of the PR's purpose here. ### Checklist - [ ] Add tests - [ ] Lint - [ ] Update docstrings

mattwthompson

New (broken) Amber example

2

### Description This is the Amber example that is currently broken. I've broken it into its own PR as suggested to avoid blocking the other examples PR. I've never used...

Yoshanuikabundi

`_simple_topology_from_openmm` fails with `RecursionError` on large topologies

15

I am trying the experimental `Interchange.from_openmm()` feature and I noticed that topology creation for multi-chain proteins would fail with`RecursionError: maximum recursion depth exceeded`: ``` # using this two chain protein:...

hjuinj

Improved LAMMPS support.

2

**Description** Please describe the behavior you would like added to Interchange. Various things we've discovered about lammps files that are requiring/using some post-generation modification we would like to improve on....

mrshirts

Positions of `MonovalentLonePair` virtual sites is incorrect (does not affect simulations)

1

**Description** In the [Virtual Sites vignette](https://github.com/Yoshanuikabundi/2024_workshops/blob/main/vignettes/01-G-vsites.ipynb), I noticed that the positions Interchange produces for monovalent lone pair virtual sites is incorrect. It looks like the angle is correctly defined, but...

Yoshanuikabundi

describing pi orbitals for rings

11

[benzene_trouble.tar.gz](https://github.com/openforcefield/openff-toolkit/files/11555131/benzene_trouble.tar.gz) **Describe the bug** I'm currently trying to run simulations using the Smirnoff Forcefield in combination the virtual sites generated by the [Astex ESP DNN](https://github.com/AstexUK/ESP_DNN/tree/master/esp_dnn) but am running into some...

peterjohncherry

NADP gives some inconsistent energies across engines.

4

**Description** [NADP](https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate) (SMILES `"c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N"` according to the [PDB](https://www.rcsb.org/ligand/NAP)) has vdW energies that only agree to 2 significant figures between Amber and other engines, and bond energies that also differ substantially...

Yoshanuikabundi

Better support bond constraints in LAMMPS export

2

**Description** This information lands in the input file, not the data file. Right now this is pretty much ignored so i.e. constrained mainline force fields aren't properly exported

mattwthompson

[LAMMPS] Full unit-awareness when parsing LAMMPS outputs with drivers

3

**Description** In the current implementation of [get_lammps_energies](https://github.com/openforcefield/openff-interchange/blob/main/openff/interchange/drivers/lammps.py#L30-L106), log file parsing is hard-coded to energies of kJ/mol and has no awareness of the various [unit styles](https://docs.lammps.org/units.html) that LAMMPS supports. Currently MDConfig.write_lammps_input()...

timbernat

Make HMR simulations easier

10

If possible. It might not be so simple.

mattwthompson