OpenFreeEnergy / OpenFreeEnergy/feflow

Create test TestNonequilibriumCyclingProtocol that uses Gaussian random numbers to quickly generate analyzable test data

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component-protocol
Dominant language
Python
Stars
20
Forks
4
PR merge metrics
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Description

In order to test our workflows, we might want to implement a very fast Protocol that generates valid nonequilibrium cycling data with analytically known results and very fast execution times.

To do this, we can sample from two harmonic oscillators with a specific free energy difference and transformation difficulty (which arises from the stddev of work values).

We can use HarmonicOscillatorsTestCase from pymbar.testsystems to do this, using code like this:

    # Generate analytical samples
    >>> testcase = HarmonicOscillatorsTestCase(O_k=[0, 1], K_k=[1, 2])
    >>> w_F, w_R, N_k = testcase.sample(N_k=[40, 50], mode='wFwR')
    # Get true free energies
    >>> analytical_free_energies = testcase.analytical_free_energies()

To make sure the free energies are reproducible, we could extract the dimensionless harmonic oscillator centers (O_k) and spring constants (K_k) for each harmonic oscillator from the transformation inputs so that they are deterministic and depend on the inputs for each ligand.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Read pymbar/testsystems/harmonic_oscillators.py and trace the Protocol entry point used by the repository's workflows. Use HarmonicOscillatorsTestCase as the reference for generating valid nonequilibrium cycling data, with oscillator parameters derived deterministically from transformation inputs. Done means the new TestNonequilibriumCyclingProtocol produces fast, reproducible data with analytically known free energies.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
testing-qa
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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