diff --git a/perses/app/setup_relative_calculation.py b/perses/app/setup_relative_calculation.py
index c43ff6054..46974c01a 100644
--- a/perses/app/setup_relative_calculation.py
+++ b/perses/app/setup_relative_calculation.py
@@ -753,7 +753,7 @@ def run_setup(setup_options, serialize_systems=True, build_samplers=True):
 def run(yaml_filename=None, override_string=None):
     cli_tool_name = sys.argv[0].split(os.sep)[-1]
     if cli_tool_name == "perses-relative":
-        warnings.warn("perses-relative will be removed in 0.11, see https://github.com/choderalab/perses/tree/main/examples/new-cli for new CLI tool", FutureWarning)
+        warning.warn("perses-relative will be removed in 0.11, see https://github.com/choderalab/perses/tree/main/examples/new-cli for new CLI tool", FutureWarning)
     _logger.info("Beginning Setup...")
     if yaml_filename is None:
        try:
@@ -954,6 +954,7 @@ def run(yaml_filename=None, override_string=None):
                 logZ[phase] = hss_run._logZ[-1] - hss_run._logZ[0]
                 free_energies[phase] = hss_run._last_mbar_f_k[-1] - hss_run._last_mbar_f_k[0]
                 _logger.info(f"\t\tFinished phase {phase}")
+                del hss[phase].energy_context_cache, hss[phase].sampler_context_cache
 
             for phase in free_energies:
                 print(f"Comparing ligand {setup_options['old_ligand_index']} to {setup_options['new_ligand_index']}")
@@ -984,6 +985,7 @@ def run(yaml_filename=None, override_string=None):
                 _logger.info(f"\n\n")
 
                 _logger.info(f"\t\tFinished phase {phase}")
+                del hss[phase].energy_context_cache, hss[phase].sampler_context_cache
 
 
 def _resume_run(setup_options):
@@ -1018,6 +1020,7 @@ def _resume_run(setup_options):
             logZ[phase] = simulation._logZ[-1] - simulation._logZ[0]
             free_energies[phase] = simulation._last_mbar_f_k[-1] - simulation._last_mbar_f_k[0]
             _logger.info(f"\t\tFinished phase {phase}")
+            del simulation.sampler_context_cache, simulation.energy_context_cache
         for phase in free_energies:
             print(f"Comparing ligand {setup_options['old_ligand_index']} to {setup_options['new_ligand_index']}")
             print(f"{phase} phase has a free energy of {free_energies[phase]}")
@@ -1041,6 +1044,7 @@ def _resume_run(setup_options):
             simulation.extend(n_iterations=left_to_do)
             _logger.info(f"\n\n")
             _logger.info(f"\t\tFinished phase {phase}")
+            del simulation.sampler_context_cache, simulation.energy_context_cache
     else:
         raise("Can't resume")