Merge pull request #835 from choderalab/ions_in_nosolv

Make Analysis only particles include ions

Yank/experiment.py

@@ -280,7 +280,9 @@ def create_alchemical_phase(self):
             checkpoint_interval = self.options['checkpoint_interval']
             # Get the solute atoms
             if self.options['store_solute_trajectory']:
-                solute_atoms = self.topography.solute_atoms
+                # "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
                 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"