[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
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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