OpenFreeEnergy / OpenFreeEnergy/openfe_analysis
Torsion Sampling
- Dominant language
- Python
- Stars
- 20
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
Type
System sampling check
Question
Is phase space well sampled?
How
Minima sampled ~60%
Tool
MDA + rdkit
Note
Ideally what you should be looking at here is a combination of the solvent, vacuum, and complex differences and the variation in dihedral sampling across lambda states. I.e. is there a major change happening in my transformation that isn't being sampled across all states -- @IAlibay
Contributor guide
No contributing guide indexed for this repository
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 reviewing the open linked pull request #20 and the existing MDA and rdkit analysis it changes. Compare solvent, vacuum, and complex results, then inspect dihedral sampling across lambda states to determine whether the transformation is adequately sampled. Done means the sampling check answers the phase-space question with evidence across these conditions.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100