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 <jalem...@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 <alexanderwie...@gmail.com>
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: <gmx-us...@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
jalem...@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-requ...@gromacs.org.
--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594
--
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-requ...@gromacs.org.
