Hi, So what should we document in the help text as the meaning, so we don't keep having emails about this?
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> > . > 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? 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.