OpenFreeEnergy / OpenFreeEnergy/feflow
Implement ATM protocol
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 20
- Forks
- 4
- PR merge metrics
- No merged PRs in 30d
Description
An implementation of a protocol that uses ATM is desired now that the new Openmm 8.1 release includes the ATMForce class for this specific purpose.
From @jchodera
Recent de Fabritiis ATM paper:
https://doi.org/10.1021/acs.jcim.3c00178
I think they used a simplified version of restraints, but there are probably lots of other choices that work fine to align the molecules if needed.
They also restrained the protein Ca atoms…
Contributor guide
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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 requested ATM protocol, OpenMM 8.1's ATMForce class, and the linked de Fabritiis ATM paper. Determine the protocol's restraint and protein Cα choices from those references, then define the implementation scope and completion criteria; the issue names no files or tests.
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Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100