[gmx-users] trjcat skipping frames

[Jared James Thompson]

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