[gmx-users] hbond error

[Mark Abraham]

Hi,

Great. To check that I understand you, do you think it should it read
"Ordering is the reverse of that in -hbn index file?"

Mark

On Thu, Feb 16, 2017 at 2:32 PM <chiara.parravicini at guest.unimi.it> wrote:

> Hi,
>
> I just realized that the hbond tool works fine, but produces output in
> reverse order. The "bug" is in the manual that states:
>
>   * -hbm:  existence matrix for all hydrogen bonds over all frames, this
> also
>     contains information on solvent insertion into hydrogen bonds.
> Ordering is
>     identical to that in -hbn index file.
>
> Chiara
>
> Il 16/02/17 13:41, *Mark Abraham * <mark.j.abraham at gmail.com> ha scritto:
> > Hi,
> >
> > I'm not sure whether I properly understand your description of the
> > behaviour. But if you think you have a case where the tool doesn't do
> what
> > its documentation says, please open an issue at
> > https://redmine.gromacs.org
> > and attach a tarball of files that will help us diagnose and fix it :-)
> >
> > Mark
> >
> > On Thu, 16 Feb 2017 13:01 Chiara Parravicini <
> > chiara.parravicini at guest.unimi.it> wrote:
> >
> > > Dear Gmx users,
> > >
> > > using GROMACS version 2016.1, I found the following error in the
> > output of
> > > the gmx hbond routine: when computed from different groups, where
> > one is a
> > > subset of the other one, hbonds from the same acceptor/donor pair do
> not
> > > match.
> > >
> > > I known that this error has been already widely discussed in previous
> > > gromacs versions. Is there any solution?
> > >
> > > Thanks
> > >
> > > Chiara
> > >
> > >
> > >
> > > --
> > > Chiara Parravicini, PhD
> > > Laboratorio di Biochimica e Biofisica Computazionale
> > > Dipartimento di Scienze Farmacologiche e Biomolecolari
> > > Università degli Studi di Milano
> > > Via Balzaretti 9,
> > > 20133 Milano, Italy
> > > Tel: +39 02-503-18256/18355
> > > Fax: +39 02-503-18284
> > >
> > >
> > > --
> > > 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-request at 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-request at gromacs.org.
> --
> Chiara Parravicini, PhD
> Laboratorio di Biochimica e Biofisica Computazionale
> Dipartimento di Scienze Farmacologiche e Biomolecolari
> Università degli Studi di Milano
> Via Balzaretti 9,
> 20133 Milano, Italy
> Tel: +39 02-503-18256/18355
> Fax: +39 02-503-18284
>
>
> --
> 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-request at gromacs.org.