Hi, I am analyzing hydrogen bonds using g_hbond. I have selected two non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and H is the hydrogen), and the other is oxygens on PO4^3- (where F is the acceptor). I am using the switch -noda, which tells the program to take the -r value as the Hydrogen-Acceptor distance (here, H-O), rather than the Donor-Acceptor distance (here, O-O). My trajectory is 10 ns long.
In the output after the calculation, I see the following: Found 233 different hydrogen bonds in trajectory Found 224 different atom-pairs within hydrogen bonding distance Can you please help me to understand the terms "hydrogen bond" and "atom-pair within hydrogen bonding distance" conceptually? I think that in order for a hydrogen and an acceptor to be considered hydrogen bonded, two criteria must be satisfied: (1) the distance (in this case, the distance between the hydrogen and the acceptor, since I am using -noda) must be less than the cutoff distance -r, and (2) the Acceptor-Donor-Hydrogen angle must be less than the cutoff angle -a. So distance and angle are the two criteria that must be met, according to g_hbond and most definitions of hydrogen bonding. So, apparently, g_hbond found 233 hydrogen bonds satisfying both the distance and angle criteria. But, g_hbond "found 224 different atom-pairs within hydrogen bonding distance." My guess is that this means that there are 224 atom pairs satisfying the distance criterion (i.e., Hydrogen-Acceptor pairs within the cutoff distance, -r). But if my interpretation of the term "atom-pair within hydrogen bonding distance" is correct, how can there be 9 _fewer_ atom pairs that satisfy only the distance criterion (and not the angle criterion), than those that satisfy _both_ the distance criterion _and_ the angle criterion? Probably, I have the wrong pictures of the terms "hydrogen bond" and "atom-pair within hydrogen bonding distance" in my head. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- 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
