dampened interactions in alchemical region

[askusay]

Hello,

I have been doing some testing in OMM_tools and noticed that setting up a part of the protein as an alchemical region massively dampens motions/interactions for this and surrounding parts. Please find attached simulation files and link to Jupyter-notebook for simulation set-up and RMSF analysis.

Red region denotes alchemical atom for alchemical simulation:

notebook: https://gist.github.com/askusay/f5601b3db1e21e6c72bf556a452020e8

So Far I have narrowed this to the alchemical NB interactions when setting up an alchemical system as setting systems based on alchemical regions where only alchemical_torsions are provided doesn't cause this issue.

Things I have tried without success so far:

1. setting up the alchemical factory with ‘direct-space’, ‘coulomb’, ‘exact’ electrostatic treatment
2. setting up the alchemical factory with consistent_exceptions set to True or False
3. Applying alchemical state through context
4. Running the simulation in vaccum as opposed implicit solvent

I would really appreciate your help. sim_files.zip