Make sure analysis_particle_indices are passed in the correct order to reporter
@@ -234,7 +234,7 @@ class AlchemicalPhaseFactory(object):
if self.options['store_solute_trajectory']:
# "Solute" is basically just not water. Includes all non-water atoms and ions
# Topography ensures the union of solute_atoms and ions_atoms is a null set
- solute_atoms = self.topography.solute_atoms + self.topography.ions_atoms
+ solute_atoms = sorted(self.topography.solute_atoms + self.topography.ions_atoms)
if checkpoint_interval == 1:
logger.warning("WARNING! You have specified both a solute-only trajectory AND a checkpoint "
"interval of 1! You are about write the trajectory of the solute twice!\n"
