8000 Update MACE-OpenMM interface documentation · Issue #838 · ACEsuit/mace · GitHub
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shrshr111 opened this issue Feb 28, 2025 · 1 comment
Open

Update MACE-OpenMM interface documentation #838

shrshr111 opened this issue Feb 28, 2025 · 1 comment
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@jharrymoore
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@shrshr111
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Hi,

I followed the installation steps in the MACE-OpenMM interface documentation and encountered several issues:

  1. The documentation does not indicate that I need to retrieve the mace-openmm.yml file from https://github.com/jharrymoore/openmmtools/tree/development. I had to find this manually.
  2. After installation, running the unit tests resulted in over 100 failed tests. It would be helpful if the team could review the test suite to determine whether these failures stem from issues with the package itself or incorrect documentation.
  3. The example inputs for OpenMM MD showed on the documentation contains multiple syntax errors. After correcting these errors and fixing the model file name in the provided input, I attempted to run the example from the documentation https://github.com/jharrymoore/openmmtools/tree/development/examples, but it still did not execute as expected.
  4. OpenMM-ML already supports the MACE potential, but the documentation does not reflect this.

Would it be possible for you to update the code and webpage and clarify the necessary installation steps? Thanks!
@basillicus
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Also:

  • The command to do the quick test has to use torch instead of torch_nl:

mace-md -f ejm_31.sdf --ml_mol ejm_31.sdf --model_path MACE-OFF23_small.model --output_dir md_test --nl torch --steps 1000 --minimiser ase --dtype float64 --remove_cmm --unwrap

However, still when I try to run the quick example, after fixing those things I get:

+-----------------+------------------------------------------------------+
|     Argument    |                        Value                         |
+-----------------+------------------------------------------------------+
|       file      |                      ejm_31.sdf                      |
|      ml_mol     |                      ejm_31.sdf                      |
|     run_type    |                          md                          |
|      steps      |                         1000                         |
|     padding     |                         1.2                          |
|      shape      |                         cube                         |
| nonbondedCutoff |                         1.0                          |
|  ionic_strength |                         0.15                         |
|    potential    |                         mace                         |
|   temperature   |                        298.15                        |
|    minimiser    |                         ase                          |
|     pressure    |                         None                         |
|    remove_cmm   |                         True                         |
| set_temperat
6F7B
ure |                        False                         |
|      unwrap     |                         True                         |
|    integrator   |                       langevin                       |
|     timestep    |                         1.0                          |
|    extract_nb   |                        False                         |
|     replicas    |                          10                          |
|    direction    |                       forward                        |
|   output_file   |                      output.pdb                      |
|    log_level    |                          20                          |
|      dtype      |                       float64                        |
|    output_dir   |                       md_test                        |
|       box       |                         None                         |
|     log_dir     |                        ./logs                        |
|     restart     |                        False                         |
|     decouple    |                        False                         |
|      equil      |                       minimise                       |
|   forcefields   | ['amber/protein.ff14SB.xml', 'amber14/DNA.OL15.xml'] |
|   water_model   |                        tip3p                         |
|       smff      |                         1.0                          |
|     interval    |                         100                          |
|     resname     |                         UNK                          |
|        nl       |                        torch                         |
|   max_n_pairs   |                          -1                          |
|       meta      |                        False                         |
|    model_path   |                MACE-OFF23_small.model                |
|   system_type   |                         pure                         |
|     mm_only     |                        False                         |
|    write_gmx    |                        False                         |
|   ml_selection  |                       resname                        |
+-----------------+------------------------------------------------------+
2025-03-18 17:52:17.549 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
Traceback (most recent call last):
  File "/home/david/miniconda3/envs/mace-openmm/bin/mace-md", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/david/miniconda3/envs/mace-openmm/lib/python3.11/site-packages/openmmtools/scripts/mace_md.py", line 245, in main
    system = PureSystem(
             ^^^^^^^^^^^
  File "/home/david/miniconda3/envs/mace-openmm/lib/python3.11/site-packages/openmmtools/openmm_torch/hybrid_md.py", line 953, in __init__
    self.create_system(ml_mol=ml_mol, model_path=model_path)
  File "/home/david/miniconda3/envs/mace-openmm/lib/python3.11/site-packages/openmmtools/openmm_torch/hybrid_md.py", line 970, in create_system
    tmp_model = torch.load(model_path, map_location="cpu")
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/miniconda3/envs/mace-openmm/lib/python3.11/site-packages/torch/serialization.py", line 815, in load
    return _legacy_load(opened_file, map_location, pickle_module, **pickle_load_args)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/miniconda3/envs/mace-openmm/lib/python3.11/site-packages/torch/serialization.py", line 1033, in _legacy_load
    magic_number = pickle_module.load(f, **pickle_load_args)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_pickle.UnpicklingError: invalid load key, '\x0a'.

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