[gmx-users] Fwd: gmx trjcat

[Alex]

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.