[gmx-users] Fwd: gmx trjcat

[Elton Carvalho]

Hello,

The advantage of text based trajectory files is that they are... text
based, which means that usual tools for treating text files, such as cat
and sed, can be used to treat text-based trajectories.

Concatenating .gro or .pdb files can be accomplished literally
concatenating the files: in POSIX-like systems (linux, macos and
recent enough versions of win10 (with some abuse of definitions)) a
command like 'cat *.gro > traj.gro'. If there are timestamps on the frames
(e.g. t=XXX in gro files), you may need to do some editing.

Cheers,
Elton

On Mon, Oct 28, 2019 at 12:18 PM 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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-- 
Elton Carvalho