Yes. Neighbor lists and similar structures are strictly an implementation detail. They're used to speed up calculations without changing any results. Similarly for the reordering done internally by some platforms: it's never visible to the user. The forces reported by getState() are the correct forc...

https://github.com/choderalab/openmmtools might be able to do what you want.

There aren't really "periodic coordinates", just coordinates. But if you intend your system to be periodic, you need to consider the periodicity correctly. Otherwise you'll get unexpected results if the coordinate isn't in the range you expect. Periodic boundary conditions are complicated and confus...

That expression is not periodic. It just depends on the absolute z coordinate, and has no dependence on the size of the box. Are you sure that's what you want?

Can you give the exact equation for what you want the potential to be as a function of z? If you can define it mathematically, it should be easy to translate into a custom force.

It doesn't. There are two possible workflows. One is to do your modelling in OpenMM, and then parameterize it with OpenMM. The other is to do your modelling with CHARMM, parameterize it with CHARMM, and then load the PSF file into OpenMM. OpenMM can't modify the structure loaded from the PSF while p...

The release candidate of 8.2 is now up. See https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=18880&p=0&start=0&view=&sid=d5a1dddcf6221cbe6b2145c20e6a684e for details about what's new in it. You can install it with conda or mamba using the command mamba install -c conda-forge/label/openmm_r...

PDBFixer has an applyMutations() function that might be what you want.

It seems very likely.

That's entirely inside the Python interpreter. It doesn't involve any OpenMM code.