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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