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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