The periodic box size has decreased to less than twice the nonbonded cutoff

[vemaparna]

I just changed the input files in the yank default yaml script. After running yank using amber prmtop and inpcrd files for 25 iterations , i got the following error. Unable to understand how the periodic box size decreased? Can you help me to figure out the problem

2022-09-25 21:03:01,339: Iteration 25/1000
2022-09-25 21:03:01,339: ********************************************************************************
2022-09-25 21:03:01,339: Single node: executing <function ReplicaExchangeSampler._mix_replicas at 0x7fd0af2cc0d0>
2022-09-25 21:03:01,339: Mixing replicas...
2022-09-25 21:03:01,347: Mixing of replicas took    0.008s
2022-09-25 21:03:01,347: Accepted 32498/388962 attempted swaps (8.4%)
2022-09-25 21:03:01,347: Propagating all replicas...
2022-09-25 21:03:01,347: Running _propagate_replica serially.
2022-09-25 21:03:07,902: Running _get_replica_move_statistics serially.
2022-09-25 21:03:07,903: Propagating all replicas took    6.556s
2022-09-25 21:03:07,903: Running _compute_replica_energies serially.
Traceback (most recent call last):
  File "/home/aparna/anaconda3/envs/yank1/bin/yank", line 10, in <module>
    sys.exit(main())
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/cli.py", line 73, in main
    dispatched = getattr(commands, command).dispatch(command_args)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/commands/script.py", line 155, in dispatch
    yaml_builder.run_experiments(write_status=write_status)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/experiment.py", line 751, in run_experiments
    completed[exp_index] = self._run_experiment(exp, write_status=write_status)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/experiment.py", line 3251, in _run_experiment
    built_experiment.run(n_iterations=switch_experiment_interval)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/experiment.py", line 427, in run
    alchemical_phase.run(n_iterations=iterations_to_run)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/yank/yank.py", line 1207, in run
    self._sampler.run(n_iterations=n_iterations)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 684, in run
    self._compute_energies()
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/utils.py", line 87, in _wrapper
    return func(*args, **kwargs)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1318, in _compute_energies
    new_energies, replica_ids = mpiplus.distribute(self._compute_replica_energies, range(self.n_replicas),
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 512, in distribute
    all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 512, in <listcomp>
    all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/multistate/multistatesampler.py", line 1358, in _compute_replica_energies
    compatible_energies = states.ThermodynamicState.reduced_potential_at_states(
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/states.py", line 937, in reduced_potential_at_states
    return [thermodynamic_states[0].reduced_potential(context)]
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmmtools/states.py", line 891, in reduced_potential
    openmm_state = context_state.getState(getEnergy=True)
  File "/home/aparna/anaconda3/envs/yank1/lib/python3.9/site-packages/openmm/openmm.py", line 12318, in getState
    state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
openmm.OpenMMException: The periodic box size has decreased to less than twice the nonbonded cutoff.
2022-09-25 21:03:08,386: Single node: executing <bound method MultiStateReporter.close of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7fd0abe1b580>>