OpenFreeEnergy / OpenFreeEnergy/openfe
atom_indices are not monotonically increasing
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- Python
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Description
When I run the tutorial with my own protein and small molecules, I got the following warning:
atom_indices are not monotonically increasing
So, I modified openfe/lib/python3.12/site-packages/mdtraj/core/topology.py as follows
np_indices = np.array(atom_indices) ===> np_indices = np.array(sorted(atom_indices)) (Line 94)
I wonder whether this change is problematic or not.
Thanks in advance.
P.S.:
use_dispersion_correction <= This setting means isotropic and analytical correction like DispCorr = EnerPres in Gromacs. Right?
Similarly, endstate_dispersion_correction means anisotropic and numerical correction like LJ-PME or EXP-LR in Gromacs. RIght?
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Research direction
Start by rerunning the tutorial with the reporter’s protein and small molecules, then inspect openfe/lib/python3.12/site-packages/mdtraj/core/topology.py around line 94 and the source of the monotonic-order warning. Determine whether sorting atom_indices changes required atom ordering, and clarify the meanings of use_dispersion_correction and endstate_dispersion_correction; done requires a confirmed resolution for both questions.
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
- 25/100