<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>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.</div><div><br></div><div>Erik</div><div><br></div><div><br><div><div>11 jun 2012 kl. 23.30 skrev Andrew DeYoung:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi, <br><br>I am analyzing hydrogen bonds using g_hbond. I have selected two<br>non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and<br>H is the hydrogen), and the other is oxygens on PO4^3- (where F is the<br>acceptor). I am using the switch -noda, which tells the program to take the<br>-r value as the Hydrogen-Acceptor distance (here, H-O), rather than the<br>Donor-Acceptor distance (here, O-O). My trajectory is 10 ns long.<br><br>In the output after the calculation, I see the following:<br><br>Found 233 different hydrogen bonds in trajectory<br>Found 224 different atom-pairs within hydrogen bonding distance<br><br>Can you please help me to understand the terms "hydrogen bond" and<br>"atom-pair within hydrogen bonding distance" conceptually?<br><br>I think that in order for a hydrogen and an acceptor to be considered<br>hydrogen bonded, two criteria must be satisfied: (1) the distance (in this<br>case, the distance between the hydrogen and the acceptor, since I am using<br>-noda) must be less than the cutoff distance -r, and (2) the<br>Acceptor-Donor-Hydrogen angle must be less than the cutoff angle -a. So<br>distance and angle are the two criteria that must be met, according to<br>g_hbond and most definitions of hydrogen bonding.<br><br>So, apparently, g_hbond found 233 hydrogen bonds satisfying both the<br>distance and angle criteria.<br><br>But, g_hbond "found 224 different atom-pairs within hydrogen bonding<br>distance." My guess is that this means that there are 224 atom pairs<br>satisfying the distance criterion (i.e., Hydrogen-Acceptor pairs within the<br>cutoff distance, -r). But if my interpretation of the term "atom-pair<br>within hydrogen bonding distance" is correct, how can there be 9 _fewer_<br>atom pairs that satisfy only the distance criterion (and not the angle<br>criterion), than those that satisfy _both_ the distance criterion _and_ the<br>angle criterion?<br><br>Probably, I have the wrong pictures of the terms "hydrogen bond" and<br>"atom-pair within hydrogen bonding distance" in my head.<br><br>Thank you for your time!<br><br>Andrew DeYoung<br>Carnegie Mellon University<br><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
</div>
<br></div></body></html>