Evan Pretti

An implementation of LCPO using `CustomManyParticleForce` can be found at . This includes a test input system and configuration (DHFR in implicit solvent, 2489 atoms). See lines 54-96 for the...

Thanks for identifying this issue. Our tests in the openmmforcefields repository used newly generated water force field files with the expected atom name format, but we didn't copy them over...

Changes in openmm/openmmforcefields#386 should allow the new CHARMM force field to work with other force field files that don't use its naming scheme, and also fix some lingering issues with...

`NoCutoff` passed to `ForceField.createSystem()` should prevent a cutoff from being set, *i.e.*, it should be the case that `force.getNonbondedMethod() == NonbondedForce.NoCutoff` for the `NonbondedForce`, and likewise for the `CustomGBForce`. This...

Thanks for the script. I can verify that both the `NonbondedForce` and the `CustomGBForce` are using `NoCutoff` so that shouldn't be an issue. From what it looks like, the minimization...

After looking a bit at the latest script, it seems like L-BFGS is getting stuck doing line searches. In single precision, it is able to get down to an RMS...

So CHARMM calls NAD+ `NAD`, NADH `NAI`, NADP+ `NAP`, and NADPH `NDP`. It seems like there are topologically identical residues `NAD1`, `NADH`, `NADP`, and `NDPH`, respectively, that use an older...

`Modeller` needs to be able to parameterize your whole system, including the ligand, so that it can determine van der Waals radii and charges of the atoms. If you just...

1. You should be able to pass `boxShape="octahedron"` to `Modeller.addSolvent()`; see the [documentation](https://docs.openmm.org/latest/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.addSolvent). 2. It looks like the names of the OpenMM `Residue`s are being assigned by OpenFF's `Topology.to_openmm()` [method](https://docs.openforcefield.org/projects/toolkit/en/stable/api/generated/openff.toolkit.topology.Topology.html#openff.toolkit.topology.Topology.to_openmm)....

If you want to take the OpenMM `System` and export it to GROMACS, you may be able to do this with Interchange directly and shouldn't need to use ParmEd. See...