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

[Marzinek, Jan]

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?



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.

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


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