[gmx-users] hbond error

[chiara.parravicini at guest.unimi.it]

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
> >
> >
> > --
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-- 
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