[gmx-users] Fwd: gmx trjcat

[Alex]

Hi Paul,

I though you mean converting the .gro files to .xtc file using *trjcat *(which
was my initial question), sorry about that.
I see now, I just used *trjconv* to convert gro file them to .xtc files and
then ... .

.gro ----trjconv----> .xtc ------trjcat----> .xtc(or trr)

Thanks
Alex

On Mon, Oct 28, 2019 at 11:18 AM Paul bauer <paul.bauer.q at gmail.com> wrote:

> Hello,
>
> I think I understood your problem (or at least hope so).
> The issue is that it is no longer possible to directly concatenate text
> based trajectory files, so I showed a possible way to work around the
> problem.
> You can also go back to a previous version of GROMACS to perform the
> concatenation, but I can't promise you that it will work.
>
> Please let me know if you need extra help to get this to work.
>
> @Justin, here is the change that added the check for binary file
> formats: c232242c29fb3ca63c8e1027eb70477069decdd9
>
> Cheers
>
> Paul
>
> On 28/10/2019 15:42, Alex wrote:
> > Hi,
> > Paul,
> > I guess you understood the question wrongly. I have some *.gro files and
> I
> > want to concatenate them to have a trr (or xtc) trajectory.
> >
> > Justin,
> > Yes indeed, It would be great if gmx trjcat could concatenate the gro
> files.
> >
> > Regards,
> > Alex
> >
> > On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 10/28/19 6:26 AM, Paul bauer wrote:
> >>> Hello,
> >>>
> >>> this looks like a case of misleading documentation. Can you file an
> >>> issue for this please on redmine.gromacs.org?
> >>> So that we don't forgot to fix this for the next patch release?
> >>> A possible work around for you can be that you first convert your
> >>> files to e.g. XTC format, use trjcat to combine them and convert them
> >>> back to GRO.
> >>>
> >> Out of curiosity, why was this file format removed as an input for
> >> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
> >> files to make a psuedo-trajectory for ensemble analysis was rather
> >> handy. Converting to an intermediate binary format is a workaround, but
> >> why add the extra step? Did the trjcat code need de-complicating?
> >>
> >> -Justin
> >>
> >>> Cheers
> >>>
> >>> Paul
> >>>
> >>>
> >>> On 27/10/2019 19:47, Alex wrote:
> >>>> Any comment on this, please?
> >>>> Thanks
> >>>> ---------- Forwarded message ---------
> >>>> From: Alex <alexanderwien2k at gmail.com>
> >>>> Date: Sat, Oct 26, 2019 at 9:38 AM
> >>>> Subject: gmx trjcat
> >>>> To: <gmx-users at gromacs.org>
> >>>>
> >>>>
> >>>> Dear all,
> >>>> I want to concatenate some gro file to have a trr or xtc trajectory
> file
> >>>> out of them as gro files are also acceptable as input files,
> >>>> according the
> >>>> gmx trjcat man page;
> >>>>
> >>>> Options to specify input files:
> >>>>    -f      [<.xtc/.trr/...> [...]] (traj.xtc)
> >>>>              Trajectory: xtc trr cpt *gro* g96 pdb tng
> >>>>
> >>>> So, I fed the .gro files in as input files likes;
> >>>> gmx trjcat -f c*.gro -o trajout.trr
> >>>>
> >>>> However, I get below error that;
> >>>> Fatal error:
> >>>> gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)
> >>>>
> >>>> Any comment is highly appreciated.
> >>>> Regards,
> >>>> Alex
> >>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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