[gmx-users] trjconv ndec not working

[Dawid das]

Dear All,

I have similar issue. I have created xtc file with precision of 1.0e-6 nm
and I want my gro file to have the same precision,
and I get this at the end of trjconv

Reading frame       0 time    3.000
Precision of npt-md-prod.xtc is 1e-06 (nm)

Setting output precision to 1e-06 (nm)
Last frame          0 time    3.000

So isn't there really a way to overcome that? For instance recompile
Gromacs?

Best wishes,
Dawid Grabarek

2018-04-17 18:48 GMT+02:00 Eric Smoll <ericsmoll at gmail.com>:

> Paul and Mark,
>
> Thanks for the reply! Good to know I wasn't doing anything wrong.
>
> Best,
> Eric
>
> On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
> > > >>> --
> > > >>> Gromacs Users mailing list
> > > >>>
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> > > >>>
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> > > >>>
> > > >>
> > > >>
> > > >> --
> > > >> Joe Jordan
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
> > > >> * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > > >>
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> or
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> > >
> > > --
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