Hi, The second set is pairs that are within h-bonding distance but that fails to fulfill the angular criteriion. The text output is hence somewhat misleading.
Erik 11 jun 2012 kl. 23.30 skrev Andrew DeYoung: > 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 [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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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