Computing surface yields unexpected error
- Dominant language
- C++
- Stars
- 29
- Forks
- 10
- PR merge metrics
- No merged PRs in 30d
Description
Hello,
I'm trying to compute a surface for a CG pure POPC membrane.
In pseudocode, the procedure I'm following looks like:
```
import MDAnalysis
from memsurfer import Membrane
u = MDAnalysis.Universe(pdb_file, xtc_file)
frame = u.trajectory[-1]
atoms = u.select_atoms('name PO4')
bbox = np.zeros((2,3))
bbox[1,:] = frame.dimensions[:3]
membrane = Membrane.compute(atoms.positions, atoms.resnames, bbox = bbox, periodic = True)
```
Which yields the following error
```
terminate called after throwing an instance of 'std::length_error'
what(): cannot create std::vector larger than max_size()
```
It looks like it has something to do with the box dimensions (maybe?) but I have no Idea how to fix it.
I also tried computing a surface from a random distribution of points within the same bounds as my membrane, and get the same error.
Thank you very much in advance for your help!
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Research direction
Start by reproducing the supplied Membrane.compute call with the POPC coordinates, periodic bounding box, and random points, then inspect the box-dimension and periodic-processing path that produces std::length_error. Done means the same inputs no longer terminate with the exception and surface computation completes or reports a clear input error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100