Raimondas Galvelis

I have created an environment: ``` conda env create mmh/openmm-8-beta-linux conda activate openmm-8-beta-linux conda install -c conda-forge openmmtools ``` The script above works with problem: ``` python debug_84.py /shared2/raimis/opt/miniconda/envs/openmm-8-beta-linux/lib/python3.10/site-packages/torchani/__init__.py:55: UserWarning:...

@moradza this might be a `conda` issue (https://github.com/openmm/openmm-torch/issues/88#issuecomment-1310477870). Could you try to install with `mamba`?

Here are the instructions: https://github.com/openmm/openmm-plumed#installing-the-plugin

@PedroHuertaRoque is any reason to build the plugin from the source rather than using `conda` (https://github.com/openmm/openmm-plumed#installing-the-plugin)?

This also applies to OpenMM-Torch

Currently `createMixedSystem` uses the *mechanical embedding*, where ML and MM regions interact only via non-bonded terms. This means that the peptide bonds of all the residues included into the ML...

@peastman it would make sense `createMixedSystem` to throw an exception if there is a bond between the ML and MM regions.

This is more issues for https://github.com/openmm/openmm-ml. @peastman could you move it there?