Surface charges Generalized Born (SCGB) approach combines the bests of the two worlds: the simplicity of Generalized Born models with the sound physics behind exact continuous electrostatics. Does not only SCGB provide accurate solvation energies for realistic systems, the surface charges obtained in the course of the calculation can be compared directly to those found using a boundary-element version of Poisson equation.

Recently we reported calculation of the Born radii. As soon as we were able to employ SCGB model expressions for the surface charges density to obtain the solvation energies in linear time as well. The results of the calculations and the comparison of the calculated values to the “exact” solvation energies obtained by solving Poisson Boltzmann equation we discussed in our previous post. Now we are back with the update on the calculation timings.

The graph above represents the timings of roughly 900 polar solvation energies calculations for proteins of different sizes ranging from 1000 to 25000. The classic Generalized Born results fall nicely to the expected series. The FFT-enhanced SCGB routine takes more time to calculate for small proteins. Nevertheless the calculation times definitely scales better than that of GB and gets better (in comparison) when the size of the system becomes sufficiently large.

Related posts:

1. O(N) Surface Charges Generalized Born calculation demonstration
2. Protein solvation energies and GB surface charges: perfect match!
3. Effects of the surface density on the stability of surface electrostatics models
4. Surface GB models: the ultimate test
5. O(N) SCGB solvation models: first “blood”