[gmx-users] g_hbond/g_sas - how is it calculated?

[Justin A. Lemkul]

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

========================================