OpenFreeEnergy / OpenFreeEnergy/openfe
IntegratorSettings don't all apply to the MD Protocol
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
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- Merged PRs (30d)
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Description
Looking at the IntegratorSettings, reassign_velocities, n_restart_attempts, and constraint_tolerance, don't get used in the PlainMDProtocol.
This is because the PlainMDProtocol uses a LangevinMiddleIntegrator, whilst the RFE and AFE Protocols use LangevinDynamicsMove.
The difference in use of integrators is expected, but the different classes should really be used to avoid user confusion.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading IntegratorSettings and the PlainMDProtocol, then compare how the RFE and AFE Protocols use LangevinDynamicsMove versus LangevinMiddleIntegrator. Trace reassign_velocities, n_restart_attempts, and constraint_tolerance through each setup; done means the protocol classes make their differing setting behavior explicit and avoid user confusion.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100