[gmx-users] Fwd: gmx trjcat

[Justin Lemkul]

On 10/28/19 10:42 AM, 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.

I don't think Paul misunderstood at all. The version of trjcat that 
you're using does not support an operation it once did - to concatenate 
coordinate files. You have to do an extra step, converting each .gro to 
an .xtc frame, before invoking trjcat. His solution gets around your 
problem.

-Justin

> 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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-- 
==================================================

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

==================================================