openmmtools.multistate.utils.SimulationNaNError: at abl-imatinib example

[iwatobipen]

Dear all, Thank you for sharing useful examples for yank. I got error when I run abl-imatinib example with slurm.

Traceback (most recent call last): File "/home/chem/miniconda/master/envs/openmm_env/bin/yank", line 10, in <module> sys.exit(main()) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/commands/script.py", line 155, in dispatch yaml_builder.run_experiments(write_status=write_status) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/experiment.py", line 738, in run_experiments self._generate_experiments_protocols() File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/experiment.py", line 2371, in _generate_experiments_protocols mpiplus.distribute(self._generate_experiment_protocol, File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 530, in distribute results = processing_unit.exec_tasks(task, node_distributed_args, propagate_exceptions_to, File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 386, in exec_tasks raise error openmmtools.multistate.utils.SimulationNaNError: Group 3/4 Node 1/1 received an exception from another MPI process. Original stack trace follow: Traceback (most recent call last): File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 357, in exec_tasks results.append(task(distributed_arg, *other_args, **kwargs)) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/experiment.py", line 2476, in _generate_experiment_protocol alchemical_phase = phase_factory.initialize_alchemical_phase() File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/experiment.py", line 310, in initialize_alchemical_phase alchemical_phase.equilibrate(n_iterations, mcmc_moves=mcmc_move) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/yank/yank.py", line 1195, in equilibrate self._sampler.equilibrate(n_iterations=n_iterations, mcmc_moves=mcmc_moves) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/openmmtools/multistate/multistatesampler.py", line 618, in equilibrate self._propagate_replicas() File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/openmmtools/utils.py", line 90, in _wrapper return func(*args, **kwargs) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/openmmtools/multistate/multistatesampler.py", line 1196, in _propagate_replicas propagated_states, replica_ids = mpiplus.distribute(self._propagate_replica, range(self.n_replicas), File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 530, in distribute results = processing_unit.exec_tasks(task, node_distributed_args, propagate_exceptions_to, File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 376, in exec_tasks raise error File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/mpiplus/mpiplus.py", line 357, in exec_tasks results.append(task(distributed_arg, *other_args, **kwargs)) File "/home/chem/miniconda/master/envs/openmm_env/lib/python3.8/site-packages/openmmtools/multistate/multistatesampler.py", line 1234, in _propagate_replica raise SimulationNaNError(message) openmmtools.multistate.utils.SimulationNaNError: Node 1/1: Propagating replica 0 at state 0 resulted in a NaN! The state of the system and integrator before the error were saved in explicitmpi/experiments/AblSTISTI0/nan-error-logs .... I used following yaml file `--- options: minimize: yes verbose: yes default_number_of_iterations: 3000 default_nsteps_per_iteration: 500 temperature: 300kelvin pressure: 1atmosphere default_timestep: 2.0*femtoseconds output_dir: explicit resume_setup: yes resume_simulation: yes

molecules: Abl: filepath: input/2HYY-pdbfixer.pdb STI: filepath: input/STI02.mol2 epik: select: !Combinatorial [0, 1, 2] ph: 7.4 ph_tolerance: 7.0 tautomerize: no openeye: quacpac: am1-bcc antechamber: charge_method: null

solvents: pme: nonbonded_method: PME switch_distance: 11angstroms nonbonded_cutoff: 12angstroms ewald_error_tolerance: 1.0e-4 clearance: 9*angstroms positive_ion: Na+ negative_ion: Cl-

systems: Abl-STI: receptor: Abl ligand: STI solvent: pme leap: parameters: [leaprc.protein.ff14SB, leaprc.gaff, leaprc.water.tip4pew]

protocols: absolute-binding: complex: alchemical_path: auto solvent: alchemical_path: auto

experiments: system: Abl-STI protocol: absolute-binding restraint: type: Boresch

` When I replaced alchemcial_path from 'auto' to 'lambda_electrostatics: [1.00, 0.95, .....', the caculation was worked. Are there any way to run yank with auto option? Any advice or suggestion are greatly appreciated. Thanks,

Taka