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Should have \sum_n W_nk = 1

See original GitHub issue

Hello,

I’m trying to extract the free energy from a number of yank experiments and some of them are throwing this error

WARNING: Did not converge to within specified tolerance.
max_delta = 2.964487e-03, tol = 1.000000e-12, maximum_iterations = 250, iterations completed = 249
Traceback (most recent call last):
  File "/export/home/bergazin/anaconda3/envs/sampl-2/bin/yank", line 11, in <module>
    load_entry_point('yank==0.23.7', 'console_scripts', 'yank')()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/cli.py", line 73, in main
    dispatched = getattr(commands, command).dispatch(command_args)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/commands/analyze.py", line 147, in dispatch
    single_run()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/mpi.py", line 271, in _wrapper
    return run_single_node(rank, task, *args, **kwargs)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/mpi.py", line 220, in run_single_node
    result = task(*args, **kwargs)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/commands/analyze.py", line 142, in single_run
    output = analyze.analyze_directory(args['--store'], **analyzer_kwargs)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 768, in analyze_directory
    analysis_data = auto_experiment_analyzer.auto_analyze()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 172, in make_copy
    return copy.deepcopy(wrap(*args, **kwargs))
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 681, in auto_analyze
    _ = self.get_experiment_free_energy_data()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 172, in make_copy
    return copy.deepcopy(wrap(*args, **kwargs))
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 541, in get_experiment_free_energy_data
    data[phase_name] = analyzer.analyze_phase()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/analyze.py", line 150, in analyze_phase
    Deltaf_ij, dDeltaf_ij = self.get_free_energy()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/multistate/multistateanalyzer.py", line 1898, in get_free_energy
    self._compute_free_energy()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/yank/multistate/multistateanalyzer.py", line 1855, in _compute_free_energy
    (Deltaf_ij, dDeltaf_ij) = self.mbar.getFreeEnergyDifferences()
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/pymbar/mbar.py", line 542, in getFreeEnergyDifferences
    np.exp(self.Log_W_nk), self.N_k, method=uncertainty_method)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/pymbar/mbar.py", line 1679, in _computeAsymptoticCovarianceMatrix
    check_w_normalized(W, N_k)
  File "/export/home/bergazin/anaconda3/envs/sampl-2/lib/python3.7/site-packages/pymbar/utils.py", line 360, in check_w_normalized
    (firstbad, column_sums[firstbad], np.sum(badcolumns)))
pymbar.utils.ParameterError: Warning: Should have \sum_n W_nk = 1.  Actual column sum for state 0 was 1.005054. 20 other columns have similar problems

My pymbar version is 3.0.5. Here is the YAML file I used for this calculation, the experiment logfile, and all my env packages in case it helps error_files.zip

Issue Analytics

State:
Created 4 years ago
Comments:7 (2 by maintainers)

Top GitHub Comments

2reactions

bergazincommented, Dec 18, 2019

Downgrading to pymbar version 3.0.3 has fixed this

0reactions

hannahbaumanncommented, Nov 25, 2020

I opened a new issue here: https://github.com/choderalab/pymbar/issues/419 and provided some input files! Let me know if you need more information!

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