[gmx-users] trjcat skipping frames

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 30 02:30:38 CEST 2010

Jared James Thompson wrote:
> Hi All,
> I'm having a problem with trjcat skipping frames. I saw a similar complaint
> seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has been
> incorporated into the current gromacs version.

Can you provide a link to this information?  What version of Gromacs are you 
using?  Presumably, if you're using the latest version, bugs from 2 years ago 
should be fixed.

> I have a number of short .trj files of equal length and time spacing that I want
> to cat together to form a single .trj file. I have a method for doing this using
> trjcat and trjconv. It has worked normally in the past.
> The method is as follows. Set the start time of each trajectory to be the next
> putative frame immediately following the previous trajectory, and also set the
> timestep for each frame correctly, so for .trj of 10 frames long:
> trjconv -f frame_traj_2.trr -o ftc_2.trr -t0 20 -timestep 1.0
> trjconv -f frame_traj_3.trr -o ftc_3.trr -t0 30 -timestep 1.0
> etc.
> Once all the frame_traj_x files are together, then use trjcat to cat them.
> trjcat -f ftc* -o CombinedTraj.trj 
>  However, this time that I am using it, trjcat is producing the following
> response, note the timestep shown in the File Roster and that ftc_5 is treated
> normally for some reason:
>          File                Start time       Time step
> ---------------------------------------------------------
>                 ftc_1.trr        0.000 ps        1.000 ps
>                 ftc_2.trr       20.000 ps        0.000 ps
>                 ftc_3.trr       40.000 ps        0.000 ps

Clearly something has broken down on a very fundamental level.  You set 
ftc_3.trr to have a start time of 30 ps above, but it has not worked.

Some questions that may help diagnose your issue:

1. What is the spacing of frames in your original .trr files?
2. What does gmxcheck tell you about each of your ftc_*.trr files?
3. Does passing -t0 and -timestep to trjconv in separate steps make any difference?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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