Dear GROMACS users,
I have looked into some of the literature in order to understand better implicit solvent models, in particular the generalized Born formalism. I believe that section 3.18 of the v4.5 GROMACS manual, dealing with the above, is in need of some corrections: 1) In eq. 3.135, the sum should run over all pairs i,j, in particular allowing i=j; there should be a corresponding factor of 1/2, and, depending on the conventions used, perhaps also a minus sign. See e.g. eq. 5 in Still et al., J. Am. Chem. Soc. 112 (1990), http://pubs.acs.org/doi/pdf/10.1021/ja00172a038. 2) In eqs. 3.137 and 3.138, x should be replaced by x_{ij}. 3) It might be better to add explicitly that \xi(x) = 1/\sqrt{x^2 + exp(-x^2/4)}, and that \xi(x) ~ 1/x for x >> 1 and \xi(x) ~ 1 for 0 <= x << 1. What do you think?
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