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With exact treatment of PME electrostatics, computing the energy matrix required for MBAR is very expensive. We can compute the optimization discussed in choderalab/yank#678 and choderalab/sams#9: i.e., split the alchemical forces into different groups and compute the energy of only the groups that are different. Here's how I plan to add the feature:
- Add option
split_force_groupsinAbsoluteAlchemicalFactory.__init__()to split forces by alchemical variable. - Require
ComposableStatesto implement a method_find_force_groups_to_update(context, context_thermodynamic_state)that figures out which force groups need to be computed to obtain the difference of potential energy. - Add a classmethod
ThermodynamicState.reduced_potential_at_states(context, thermodynamic_state_list)that uses the method above to efficiently compute the reduced potential at all the given thermodynamic states.
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