ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Free rotor in force field?
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- Dominant language
- Python
- Stars
- 51
- Forks
- 25
- Avg merge
- 4d 5h
- Merged PRs (30d)
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Description
Force field conformer jobs of prenol, 2,3-dimethylbut-2-ene and their radicals, RO2, RO2H, OOQOOH indicates they could possess free CH3 rotors in MMFF94s. Here, I provide an example of prenol.
2D structure
3D structure
ARC default conformer torsions result (500 random conformers)
When applying 10000 random conformers:
When checking exact dihedral angles for the lowest 5 conformers of both samplings, dihedrals are indeed different (see below). For 10000 sampling, FF_energy are equal; for 500 sampling, the difference only appears at 10th digit after decimal points
It seems like there is no well for the two alkenyl methyl groups (H3C-C=C). I am not sure about the influence of this kind of behavior. (This may enlarge the conformer search space?). So far I haven't had the ab initio result yet.
Contributor guide
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First steps
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Research direction
The report does not identify a source file, test, or entry point. Reproduce the prenol force-field conformer jobs with 500 and 10,000 random conformers, then compare the methyl torsions and energies; done should establish whether the apparent free rotors are expected and whether they affect conformer searching.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- performance, tooling
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100