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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