[gmx-users] trjconv ndec not working

[Dawid das]

The quick and dirty solution is that I write gro and g96 and copy
coordinates from the latter to the former, but I'd rather
have more elaborate solution.

2018-04-18 14:53 GMT+02:00 Dawid das <addiw7 at googlemail.com>:

> 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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>> > > >>>
>> > > >>
>> > > >>
>> > > >> --
>> > > >> Joe Jordan
>> > > >> --
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>
>