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5. Fixed charge from structure

5. Fixed charge from structure

From the paper/ESI (see also knowledge/04-clya-geometry-and-charge/index.md):

  • CHARMM36 partial charges and radii, protonation at pH 7.5 via PROPKA + PDB2PQR.
  • Per-atom Gaussian smearing with σ_i = 0.5 · R_i (sharpness factor 0.5 × atomic radius).
  • Ensemble of 50 aligned MD frames from the final 5 ns of a 30 ns run (VMD RMSD alignment).
  • Azimuthal contribution δ_i / (2π r_i); gridded at 0.005 nm; loaded as a linear interpolation function rhoq_pore(r,z).
  • Axis guard, verbatim COMSOL: scd_pore = if(r < 0.01[nm], 0, e_const * rhoq_pore(r,z) / (2*pi*r)) [C m⁻³].

The density map used for the geometry is a separate object: 0.5 Å grid, per-atom Gaussian using each atom's VdW radius with width factor σ = 0.93, radially averaged, pore surface taken as the 25 % contour. Do not confuse the two sharpness factors (0.93 for the geometry density, 0.5 for the charge smearing).