[gmx-users] Generalized Born in GROMACS manual

Ehud Schreiber schreib at compugen.co.il
Mon Nov 8 16:49:32 CET 2010

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),

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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