[gmx-users] Questions about GB parameters

[Justin A. Lemkul]

Hi All,

I wanted to dig up an old discussion that hit the list a long time ago because 
I'm now encountering some problems understanding the GB settings myself.  The 
discussion in question is here:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html

I wanted to post a couple of questions based on Per's response.

1. Based on that post, it seems to me that the value in the gbr column should 
have a dielectric offset added to it during the GB calculations.  In the code, 
though (genborn.c, around line 484 in the latest release-4-5-patches), it looks 
like the dielectric offset is subtracted, not added.  I guess the code is 
reversing the process, going from GB radius back to vdW radius by subtracting 
the dielectric offset?  It seems, then, that the parameters in gbsa.itp should 
specify GB radii, not vdW radii, though the manual says the gbr column is 
"atomic van der Waals radii, which are used in computing the Born radii."  Is 
the opposite actually true?

2. I am still unclear on the source of the HCT scaling factors.  From the 
reference cited in the manual, it would seem that scaling factors are 
interaction-dependent, at least when H atoms are concerned.  I also cannot find 
any indication of where these values came from.  None of the values of Table 2 
in the HCT reference match the contents of the "hct" column.  Again I wonder if 
I'm missing something obvious :)

Thanks for any insight!

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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