[gmx-users] g_hbond/g_sas - how is it calculated?
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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond/g_sas - how is it calculated?
On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan j.marzine...@imperial.ac.uk 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond/g_sas - how is it calculated?
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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
