Gmx trjcat

User discussions
1

GROMACS version:2023
GROMACS modification: Yes/No
I am using gmx trjcat to combine ten trajectories into one (gmx trjcat -f step6_1.trr step6_2.trr step6_3.trr step6_4.trr step6_5.trr step6_7.trr step6_8.trr step6_9.trr step6_10.trr -o ixed.trr -settime) each trajectory is 1ns =1000ps

The prompt i got is shown below. after doing this i got an output file ixed.trr and used analysis tool (rms ) (gmx rms -s step6_1.tpr -f ixed.trr -o rmsd.xvg) then i tried to plot it but what igot is an empty plot what is the problem?
Command line:
gmx trjcat -f step6_1.trr step6_2.trr step6_3.trr step6_4.trr step6_5.trr step6_7.trr step6_8.trr step6_9.trr step6_10.trr -o ixed.trr -settime

trr version: GMX_trn_file (single precision)
Reading frame 1 time 10.000
File Current start (ps) New start (ps)

          step6_1.trr        0.000 ps          Note that major changes are planned in future for trjcat, to improve usability and utility.0 
          step6_2.trr        0.000 ps          1001 
          step6_3.trr        0.000 ps          2001
          step6_4.trr        0.000 ps          3001
          step6_5.trr        0.000 ps          4001
          step6_7.trr        0.000 ps          5001
          step6_8.trr        0.000 ps          6001
          step6_9.trr        0.000 ps          7001
         step6_10.trr        0.000 ps          8001

Summary of files and start times used:

      File                Start time       Time step

          step6_1.trr        0.000 ps       10.000 ps
          step6_2.trr     1001.000 ps       10.000 ps
          step6_3.trr     2001.000 ps       10.000 ps
          step6_4.trr     3001.000 ps       10.000 ps
          step6_5.trr     4001.000 ps       10.000 ps
          step6_7.trr     5001.000 ps       10.000 ps
          step6_8.trr     6001.000 ps       10.000 ps
          step6_9.trr     7001.000 ps       10.000 ps
         step6_10.trr     8001.000 ps       10.000 ps

Back Off! I just backed up ixed.trr to ./#ixed.trr.1#
Reading frame 0 time 0.000
lasttime 0

Continue writing frames from step6_1.trr t=0 ps, frame=0
Last frame 100 time 1000.000 → frame 90 time 900.000 ps
Reading frame 0 time 0.000
lasttime 990

Continue writing frames from step6_2.trr t=1001 ps, frame=100
Last frame 100 time 1000.000 → frame 190 time 1901.000 ps
Reading frame 0 time 0.000
lasttime 1991

Continue writing frames from step6_3.trr t=2001 ps, frame=200
Last frame 100 time 1000.000 → frame 290 time 2901.000 ps
Reading frame 0 time 0.000
lasttime 2991

Continue writing frames from step6_4.trr t=3001 ps, frame=300
Last frame 100 time 1000.000 → frame 390 time 3901.000 ps
Reading frame 0 time 0.000
lasttime 3991

Continue writing frames from step6_5.trr t=4001 ps, frame=400
Last frame 100 time 1000.000 → frame 490 time 4901.000 ps
Reading frame 0 time 0.000
lasttime 4991

Continue writing frames from step6_7.trr t=5001 ps, frame=500
Last frame 100 time 1000.000 → frame 590 time 5901.000 ps
Reading frame 0 time 0.000
lasttime 5991

Continue writing frames from step6_8.trr t=6001 ps, frame=600
Last frame 100 time 1000.000 → frame 690 time 6901.000 ps
Reading frame 0 time 0.000
lasttime 6991

Continue writing frames from step6_9.trr t=7001 ps, frame=700
Last frame 100 time 1000.000 → frame 790 time 7901.000 ps
Reading frame 0 time 0.000
lasttime 7991

Continue writing frames from step6_10.trr t=8001 ps, frame=800
Last frame 100 time 1000.000 → frame 900 time 9001.000 ps

Last frame written was 900, time 9001.000000 ps

2

Firstly, you should be aware that you are only concatenating nine files not ten (step6_6.trr is missing).

Does the trajectory file open in, e.g., vmd?