[gmx-users] Questions about GB parameters

[Justin A. Lemkul]

Can anyone comment further on either of these issues?

-Justin

Mark Abraham wrote:
> On 15/06/2011 4:24 AM, Justin A. Lemkul wrote:
>>
>> 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?
> 
> It does look to me as though something is mis-sense here. The quantity 
> given in gb_dielectric_offset is always subtracted from a value that I 
> think is found in the gbr column of [implicit_genborn_parameters].
> 
> Mark
> 
>> 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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