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.
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
ftc_4.trr 60.000 ps 0.000 ps
ftc_5.trr 80.000 ps 1.000 ps
Back Off! I just backed up CombinedTraj.trr to ./#CombinedTraj.trr.3#
Reading frame 0 time 0.000
Continue writing frames from ftc_1.trr t=0 ps, frame=0
Last frame 20 time 20.000 -> frame 10 time 10.000 ps
Reading frame 0 time 20.000
lasttime 19
Continue writing frames from ftc_2.trr t=20 ps, frame=20
Last frame 0 time 20.000
WARNING: Frames around t=20.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frame 0 time 40.000
lasttime 20
Continue writing frames from ftc_3.trr t=40 ps, frame=21
Last frame 0 time 40.000
WARNING: Frames around t=40.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frame 0 time 60.000
lasttime 40
Continue writing frames from ftc_4.trr t=60 ps, frame=22
Last frame 0 time 60.000
WARNING: Frames around t=60.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frame 0 time 80.000
lasttime 60
Continue writing frames from ftc_5.trr t=80 ps, frame=23
Last frame 20 time 100.000 -> frame 40 time 97.000 ps
Last frame written was 43, time 100.000000 ps
------------------------------------------------
Any help would be appreciated.
Best,
Jared Thompson
--
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN 47907-2091
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