[gmx-users] trjcat skipping frames
Jared James Thompson
thompsjj at purdue.edu
Fri Jul 30 20:56:04 CEST 2010
The old information is given below. I haven't chopped into the code yet to see
if Berk's fix is there.
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> Jared James Thompson wrote:
> > Hi All,
> > I'm having a problem with trjcat skipping frames. I saw a similar
> > seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has
> > 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
> > to cat together to form a single .trj file. I have a method for doing this
> > 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
> > putative frame immediately following the previous trajectory, and also set
> > 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
> > 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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN 47907-2091
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