[gmx-users] trjcat with settime option using command line

Justin Lemkul jalemkul at vt.edu
Thu Apr 16 01:06:15 CEST 2015

On 4/15/15 10:33 AM, Rebeca García Fandiño wrote:
> Dear GROMACS users,
> I am trying to concatenate several trajectories
> with identical times using the command trjcat with the options -cat and
> -settime. I have to introduce manually the option "c" each time a new
> trajectory is read. I would like to introduce this line into a script,
> in such way I could do it automatically. I have tried:
> echo c c c | trjcat -s minimizado.tpr -f trajectory1.xtc trajectory2.xtc trajectory3.xtc -cat -settime
> and also
> trjcat
>   -s minimizado.tpr -f trajectory1.xtc trajectory2.xtc trajectory3.xtc
> -cat -settime < input_file (where input_file contains the line "c c
> c")
> But in both cases it does not work. I get the error:
> Program trjcat, VERSION 5.0.4
> Source code file: /root/gromacs-5.0.4/src/gromacs/gmxana/gmx_trjcat.c, line: 220
> Fatal error:
> Error reading user input
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Is there any way to give this information to trjcat through a command line?

The problem probably comes from using -s, which is not a valid option to trjcat.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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