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

Rebeca García Fandiño regafan at hotmail.com
Wed Apr 15 16:33:46 CEST 2015

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  

 -s minimizado.tpr -f trajectory1.xtc trajectory2.xtc trajectory3.xtc 
-cat -settime < input_file (where input_file contains the line "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?

Thanks a lot for your help


Dr. Rebeca Garcia
Santiago de Compostela University

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