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
--
========================================
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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