Hello all,
Please, what is the current status of the periodic boundary conditions in
UFF implementation? I saw PR in the version 3.
In case it's working, how can I make use of it? I am now trying to compute
energy of a periodic, crystalline structure, where I "manually" create
bonds across the PBC, but this results in disaster. Removing the bonds
across the PBC makes it better, but I have no clue whether it's because it
works then and UFF guesses the bonds automatically or because I've got
non-bonded atoms.
I use python, with recently installed conda version of openbabel (version
in the __init__ file says it should indeed be 3.0.0). Here is my code:
from openbabel import openbabel as ob
obmol = ob.OBMol()
conv = ob.OBConversion()
conv.SetInAndOutFormats('pdb', 'pdb')
conv.ReadFile(obmol, "SiO2.pdb") #this is the .pdb file with bonds
across the PBC
ff = ob.OBForceField.FindForceField("UFF")
ff.Setup(obmol)
ff.Energy()
ff.ConjugateGradients(5000)
ff.GetCoordinates(obmol)
conv.WriteFile(obmol, "optimized.pdb")
Thank you!
tags: UFF, unit cell, periodic box, periodic boundary conditions, PBC
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