[gmx-users] Questions about GB parameters

[Per Larsson]

Hi!

Hmm.. Let me see if I can shed some more light on this. It's been a while though since I visited the literature here, and also my laptop broke down today, so I need to take of that first before I can check the code!

Thanks
/Per


14 jun 2011 kl. 20:24 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:

> 
> 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
> 
> -- 
> ========================================
> 
> 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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