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Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.

Home Page: https://apallath.github.io/pyves

License: MIT License

Shell 0.15% Python 99.85%
enhanced-sampling optimization machine-learning variational-method pytorch langevin-dynamics openmm

pyves's Introduction

pyves

Flowchart of options

graph LR;
    1[Choose Basis]-->A(Legendre polynomial)-->AA[Choose basis size];
    1-->B(Neural network)-->BB[Choose network architecture];

    2[Choose Target]-->C(Uniform distribution);
    2-->D(Well-tempered distribution)-->D1[Choose bias factor];
    D-->D2[Choose free energy localization]
    D2-->D2A(No localization)
    D2-->D2B(Localized with sigmoidal cutoff)

    3(Update)-->E[Choose averaging method]
    E-->E1(Instantaneous)
    E-->E2(Running average)
    E-->E3(Weighted running average)-->E3A[Choose exponent]
    E-->E4(Moving window average)-->E4A[Choose window size]

    3-->F[Choose optimizer]
    F-->F1(Stochastic PyTorch optimizers)
    F-->F2(Original VES 2nd order optimizer)

    3-->G[Choose learning rate]
    G-->G1[Choose learning rate decay]
    G1-->G1A(No decay)
    G1-->G1B(Decay below KL-divergence cutoff)
    G1B-->G1B1[Choose cutoff]
    G1B-->G1B2[Choose exponent]
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pyves's People

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pyves's Issues

Ignore .DS_Store

Quick gitignore fix - remember to make this during next commit.

Legendre poly fix

Current implementation involves performing an inplace operation on a leaf variable. Either fix, or move to explicit representation instead of recurrence relation.

Check scaling

Consider adding explicit scaling to the force, remove from update.

Hooks and actions

  • Add pre-commit hooks to automatically generate docs
  • Add Github actions to run tests

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