OpenFreeEnergy / OpenFreeEnergy/openfe
Default solvent padding is often nsufficient for solute-only dodecahedron boxes.
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- Dominant language
- Python
- Stars
- 332
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Our default 1.2 nm solvation usually works fine when working on cubic boxes, but can lead to the following error when using dodecahedron boxes:
openmm.OpenMMException: The periodic box size has decreased to less than twice the nonbonded cutoff.
The current solution to this problem is to use a larger cutoff for solute-only calculations with dodecahedrons - usually 1.5 nm works.
This may be related to #827, specifically @mattwthompson's comment regarding the bounding box issues with small molecules.
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 reproducing a solute-only calculation with a dodecahedron box and the current 1.2 nm default, using the reported OpenMM periodic-box error as the failure condition. Compare this with the 1.5 nm workaround and review the related bounding-box discussion in issue #827; the work is done when the default no longer produces the cutoff error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100