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<p class=MsoNormal>Dear GROMACS users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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: <o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span dir=LTR></span>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.<br>
See e.g. eq. 5 in Still et al., J. Am. Chem. Soc. 112 (1990), <a
href="http://pubs.acs.org/doi/pdf/10.1021/ja00172a038">http://pubs.acs.org/doi/pdf/10.1021/ja00172a038</a>.<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span dir=LTR></span>In eqs. 3.137 and 3.138, x should
be replaced by x_{ij}.<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span dir=LTR></span>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.<o:p></o:p></p>
<p class=MsoNormal>What do you think?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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