[gmx-users] g_hbond/g_sas - how is it calculated?
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 8 16:55:13 CEST 2011
Marzinek, Jan wrote:
> Hi,
>
>
>
> I have a question related to the calculation of hydrogen bonds in
> Gromacs. As I read in Manual it comes from the distance between donor
> and acceptor ( <= 0.35 nm) and the angle <=30 degr beween hydrogen and
> acceptor. The question is - why 30 degr? How is it related to the reality?
>
>
Hydrogen bond strength decreases with distance between the donor and acceptor
and with deviation from linearity. A survey of crystallographic structures
shows that these are generally accepted criteria. There is literature on this
that dates back many decades.
>
> The second thing is the claculation of the accessible surface area
> (g_sas) of the molecule for instance? It is not explained in manual and
> I am really curious how g_sas makes these calculations.
>
I'd suggest you look at the citation provided in the "PLEASE READ AND CITE THE
FOLLOWING REFERENCE" section printed when running g_sas :)
-Justin
> As my supervisors do not know the gromacs their questions are always
> about such details :)
>
> However, I think it is really important to understand what you are
> really doing using commands in Gromacs which provide you with really
> detailed results.
>
>
>
> Thank you in advance,
>
>
>
> Jan
>
>
>
--
========================================
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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