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Draft: Trim atoms in OpenMM

Jonathan Barnoud requested to merge feature/trim-atoms into master

Allow to only transmit the N first atoms of an OpenMM simulation with N given by the user. This is especially relevant for simulation in explicit solvent as it allows to not transmit the solvent for better performances.

This PR adds the --end argument to narupa-omm-server and makes the changes for the argument to be taken into account.

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