[gmx-users] trjconv ndec not working

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 17 18:08:24 CEST 2018


Hi,

What Paul said agrees with my memory, but I'd not found time to check that
yet. We should indeed fix the docs.

Mark

On Tue, Apr 17, 2018, 16:42 Paul Bauer <paul.bauer.q at gmail.com> wrote:

> Hello Eric,
>
> I had a look at the code for writing gro files and it looks to me that
> it is only able to write three decimal places there.
> There is a comment in the code that mentions that writing other
> precisions has been removed.
> This means that we need to update the man page text to not be confusing.
>
> Cheers
>
> Paul
>
>
> On 2018-04-15 17:45, Eric Smoll wrote:
> > Hello Joe,
> >
> > Thanks for the reply. Sorry if I was not clear. I provide a gro file
> with high precision (7 decimal places). For some reason, the output gro
> always has three decimal places. The manual   for trjconv suggests that the
> output should have 7 decimal places.
> >
> > Best,
> > Eric
> >
> >> On Apr 15, 2018, at 4:00 AM, Joe Jordan <e.jjordan12 at gmail.com> wrote:
> >>
> >> Are you trying to write from an xtc file? If so, does it have the
> necessary
> >> precision?
> >>
> >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll <ericsmoll at gmail.com>
> wrote:
> >>>
> >>> Hello Gromacs Users,
> >>>
> >>> I am using Gromacs 2018.1.
> >>>
> >>> The manual page for gmx trjconv states the number of decimal places in
> the
> >>> output of a gro file is taken from the number of decimal places in the
> >>> input unless the ndec flag is set. The ndec flag can be used to
> increase
> >>> precision in the output.
> >>>
> >>> However, providing trjconv a gro file with increased coordinate
> precision
> >>> (7 decimal places) does not increase the precision of the output gro
> file.
> >>> Also, the ndec flag has no impact on the output precision.
> >>>
> >>> My input gro is written as follows:
> >>>
> >>> comment
> >>> 10
> >>>     1ABC     C1    1  -0.1204914  -0.0759159  -0.0131147
> >>> ...etc.
> >>>
> >>> trconv does not complain about this file format and creates a normal,
> three
> >>> decimal
> >>> gro file as output.
> >>>
> >>> Has this feature been removed?
> >>>
> >>> Best,
> >>> Eric
> >>> --
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> >>>
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> >>
> >>
> >> --
> >> Joe Jordan
> >> --
> >> Gromacs Users mailing list
> >>
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