MemSurfer
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LLNL
Computing surface yields unexpected error
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!
