openff-interchange

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Improve the conversion performance of Interchange object to LAMMPS data file

1

**Description** It takes too long to write LAMMPS data file for a medium system size. I experienced this when I tried to convert a rather big system, with 174200 atoms,...

taidbui

https://github.com/openforcefield/openff-interchange/pull/707#pullrequestreview-1482373038

Yoshanuikabundi

**Description** "out.lmp" is hardcoded, though users may reasonably wish to use different names for their files

mattwthompson

**Description** The supported thermodynamic outputs in the LAMMPS driver are [hardcoded](https://github.com/openforcefield/openff-interchange/blob/35ac30006146b9b5eb3e344660b84ffa9933f2fb/openff/interchange/components/mdconfig.py#L265). I think these cover the important bits, but it might be useful to expose these options to users.

mattwthompson

Re-write OpenMM virtual site creation to use specific classes

2

For historical reasons, all virtual sites are created using `openmm.LocalCoordinatesSite`, which does a lot of fancy math to handle all virtual sites with one object. Unfortunately, this comes at the...

mattwthompson

**Description** This example would set up and run a brief simulation of a small nucleic acid with a large surfactant molecule (too large for AM1BCC, must use NAGL) * Start...

j-wags

See the tail end of this comment for some good suggestions: https://github.com/openforcefield/openff-interchange/pull/756#issuecomment-1612478743 These changes would need to be pushed to the `central-examples` branch to go live until a release is...

mattwthompson

Support Python 3.11

1

Blockers: * No AmberTools packages * ~~No OpenEye Toolkits packages~~

mattwthompson

Add support for using customised packmol input file

5

**Description** Please describe the behavior you would like added to Interchange. Dear Dev team, Currently, the packmol features within Interchange or Evaluator enable the solvation and random placement of molecules...

taidbui

Unclear how to split OpenMM torsion energies between propers and impropers

2

OpenMM conventionally groups proper and improper torsions into the same force, from which I don't know how to split contributions from each. ```python In [23]: torsion_force Out[23]: In [24]: [val...

mattwthompson