OpenFreeEnergy / OpenFreeEnergy/openfe

How to restart MD run?

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Description

Hi,
I was wondering how to resume running MD. it is required if a previous run ended prematurely. I expected the checkpoint file to play a role somehow, but I'm getting an error.

I tried to trace the source code, but couldn't get a clue.

INFO:openfe.setup._rbfe_utils.relative:creating hybrid system
INFO:openfe.setup._rbfe_utils.relative:setting force field terms
INFO:openfe.setup._rbfe_utils.relative:adding forces
INFO:openfe.setup._rbfe_utils.relative:DONE
WARNING:openmmtools.multistate.multistatereporter:Warning: The openmmtools.multistate API is experimental and may change in future releases
DEBUG:openmmtools.multistate.multistatereporter:Initial checkpoint file automatically chosen as m10_m12/complex/rbfe_checkpoint.nc
WARNING:openmmtools.multistate.multistatesampler:Warning: The openmmtools.multistate API is experimental and may change in future releases
DEBUG:openmmtools.multistate.multistatesampler:CUDA devices available: (['0', ' NVIDIA TITAN Xp'], ['1', ' NVIDIA TITAN Xp'], ['2', ' NVIDIA TITAN Xp'], ['3', ' NVIDIA TITAN Xp'])
DEBUG:mpiplus.mpiplus:Cannot find MPI environment. MPI disabled.
DEBUG:mpiplus.mpiplus:Single node: executing <bound method MultiStateReporter.storage_exists of <openmmtools.multistate.multistatereporter.MultiStateReporter object at 0x7f449d9a4640>>
Traceback (most recent call last):
  File "run_md.py", line 159, in <module>
    transform.run(dry=False, verbose=True)
  File "/db2/users/isjoung/openfe/openfe/setup/methods/openmm/equil_rbfe_methods.py", line 917, in run
    sampler.setup(
  File "/db2/users/isjoung/openfe/openfe/setup/_rbfe_utils/multistate.py", line 143, in setup
    self.create(thermodynamic_states=thermodynamic_state_list,
  File "/db2/users/isjoung/anaconda3/lib/python3.8/site-packages/openmmtools/multistate/multistatesampler.py", line 590, in create
    raise RuntimeError('Storage file {} already exists; cowardly '
RuntimeError: Storage file m10_m12/complex/rbfe.nc already exists; cowardly refusing to overwrite.

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  3. Fork the repository and make your change on a branch.
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Research direction

Start with the traceback in run_md.py and the referenced setup code in openfe/setup/methods/openmm/equil_rbfe_methods.py and openfe/setup/_rbfe_utils/multistate.py. Check how the checkpoint and existing rbfe.nc files are handled, then document a reproducible way to resume an interrupted MD run and verify it avoids the overwrite error.

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Assessment

Tech stack
python
Domain
documentation
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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