On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan <[email protected]> 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?
It's a default value, you can change it when you need. > > > > 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. All I can say is that, practice and problems are a good teacher. > > > > Thank you in advance, > > > > Jan > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Best Regards, lina -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
