Hi, "Pairs within 0.35" has misled David, Justin and I, and doubtless others... without clarification, it is normal to assume that if a hydrogen bond is "pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would be a superset of the former. But the field is actually "pairs within 0.35 that do not satisfy the angle requirement."
Mark On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund <erik.markl...@kemi.uu.se> wrote: > Yes. The sets have no overlap. But for some reason putting that in a short > description seems difficult :-) > > > On 1 Jun 2017, at 15:31, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > > > Hi, > > > > I still don't understand your description. Is the third column > *additional* > > pairs within 0.35 that do not satisfy the angle criterion? > > > > Mark > > > > On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.markl...@kemi.uu.se> > > wrote: > > > >> > >> > >> On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se > >> <mailto:sp...@xray.bmc.uu.se>> wrote: > >> > >> On 26/05/17 22:05, Erik Marklund wrote: > >> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, > which > >> is why they are sometimes fewer than the hbonds. > >> > >> Therefore I would assume they are more instead. > >> > >> > >> They sometimes are, but not necessarily. I pointed it out because > >> sometimes people ask if g_hbond is buggy when they see that there are > >> occasionally lower numbers in the third column, assuming that it > contains > >> all pairs within 3.5 Å regardless of angle which should more numeorus > than > >> the pairs that also fullfil the angle criterion. That’s not the meaning > of > >> the third column however. > >> > >> Kind regards, > >> Erik > >> > >> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p13008...@nitc.ac.in > >> <mailto:adarsh_p13008...@nitc.ac.in>> wrote: > >> > >> Dear all, > >> > >> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " > >> > >> I would like to edit the file before viewing in 'Xmgrace' > >> > >> I opened the hbnum.xvg using 'gedit'. It shows following details (see > >> below) > >> > >> Can you please tell me what is there in the third column of the file? > >> > >> --------------------------------------------------------- > >> # gmx hbond is part of G R O M A C S: > >> # > >> # GROtesk MACabre and Sinister > >> # > >> @ title "Hydrogen Bonds" > >> @ xaxis label "Time (ps)" > >> @ yaxis label "Number" > >> @TYPE xy > >> @ view 0.15, 0.15, 0.75, 0.85 > >> @ legend on > >> @ legend box on > >> @ legend loctype view > >> @ legend 0.78, 0.8 > >> @ legend length 2 > >> @ s0 legend "Hydrogen bonds" > >> @ s1 legend "Pairs within 0.35 nm" > >> 0 2 7 > >> 10 2 5 > >> 20 4 3 > >> 30 3 2 > >> 40 3 3 > >> 50 5 1 > >> 60 3 6 > >> 70 3 6 > >> 80 2 3 > >> 90 5 1 > >> 100 3 3 > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org<mailto: > >> gmx-users-requ...@gromacs.org>. > >> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 > <018-471%2042%2005> <018-471%2042%2005> > >> . > >> http://www.icm.uu.se<http://www.icm.uu.se/> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org<mailto: > >> gmx-users-requ...@gromacs.org>. > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? 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