This FAQ entry discusses the various things that can cause that error message. I'm going to guess you have incorrect bonds. When loading a PDB file it knows to add bonds to standard residues, but if you've modified it to be nonstandard it won't know how to add the necessary bonds, and therefore it ...

Just create the System directly. system = System() for atom in topology.atoms(): system.addParticle(atom.element.mass) indices = list(range(system.getNumParticles())) numbers = [atom.element.atomic_number for atom in topology.atoms()] system.addForce(XtbForce(method, charge, multiplicity, periodic, ...

Some of your settings are very usual. For example, you set the cutoff distance to 50 A, which is huge. Values around 10 A are more typical. A timestep of 0.01 ps is larger than people typically use, but 1e-4 ps is much smaller than normally used. Setting all the particles to random initial positions...

We've released version 8.1.2. This is a patch release that fixes a few mostly minor issues. The most important one is to work around a change in the latest version of GAFF that was causing parameterization of small molecules with openmmforcefields to fail. See https://github.com/openmm/openmm/releas...

There are two parts to that question. Can you use a NNP? Yes, it's pretty easy. OpenMM-ML provides a high level interface for it. OpenMM-Torch is the lower level interface to PyTorch it's built on. Can you do FEP? There certainly are packages for doing free energy calculations with OpenMM. See for e...

simulation.step(num_steps) state.getPositions(asNumpy=True) You don't retrieve a new State object. You call getPositions() on some state you created earlier, though I don't know when or how you created it. That isn't shown in your code. If you want to get the current positions, you need to call get...

You could always install openmm-xtb and use GFN-FF. It's slower than a lot of other force field, and I can't speak for the accuracy, but it's very easy to get any system running.

This paper uses OpenMM to simulate graphene. I'm not sure if their code is available.

It's probably trying to compute the atomic charges using AM1-BCC, which is going to be pretty expensive. I haven't worked with graphene, but I think there are force fields specifically for simulating it. A web search for "graphene molecular force field" turned up lots of hits, for example https://li...

Please provide a complete example I can use to reproduce the problem. Otherwise, I don't really know what you're doing or why it isn't working!

Can you provide a complete, working example that demonstrates the problem? The code you posted before doesn't correspond to what you described since it doesn't use a real integrator, doesn't run any dynamics, and never retrieves the positions.