NonbondedForce and CustomNonbondedForce both define interactions of every particle in the system with every other. That means you need to define parameters for every particle. It's ok if some of those parameters are such that they don't actually interact, such as having a charge of 0. But you do nee...

Without introducing a biasing force? No. Anything that prevents it from rotating is, by definition, a bias. A biasing force would be a fairly standard way of handling this situation. Yes, it would affect the results compared to letting it freely rotate in the simulation box, but hopefully the differ...

Sure, you can call modeller.add() to add anything you want. You'll need to pick the ion positions yourself in that case.

Is the reason for not using addSolvent() just that you don't want to add any water? If you set numAdded to the number of ions, that will ensure it doesn't add anything else.

So far as I know, Interchange is a recently added class that just provides a different interface to the same parametrization code. For protein-ligand systems, the recommended approach is to use OpenMM's ForceField class for the protein, and add a SMIRNOFFTemplateGenerator for the ligand. See https:/...

The fact that it works correctly in double precision mode suggests it's an issue with the accuracy of calculations rather than what particular calculations it's doing. I recently fixed a bug that reduced the accuracy of some calculations in mixed precision mode. It was representing certain constants...

Interesting, I'm not sure why that is happening. The CMMotionRemover should be getting applied separately to each bead. I'll take a look and see if I can figure out what's going on.

The force field format is documented at http://docs.openmm.org/latest/userguide ... g_ffs.html. Atom types are assigned based on elements and bonds. It doesn't matter what names the atoms have, so long as the element symbol column is filled in correctly.

It sounds like the question is how to insert a particle, calculate the energy, and then remove it again? Since it's an isolated particle, I assume it isn't involved in any bonded interactions, only nonbonded ones? The simplest way of doing that is to include the extra particle in the system from the...

I'm not familiar with that algorithm. Can you describe how it works?

Thanks! By the way, your code can be simplified a bit. Instead of for i in range(system.getNumForces()): force = system.getForce(i) force.setForceGroup(i) forcename = force.getName() forcegroups[forcename] = i you can write for i, force in enumerate(system.getForces()): force.setForceGroup(i) forceg...