[gmx-users] trjcat skipping frames

[Jared James Thompson]

The old information is given below. I haven't chopped into the code yet to see
if Berk's fix is there.

http://www.mail-archive.com/gmx-users@gromacs.org/msg14689.html


~j



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
> 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
> 
> -- 
> ========================================
> 
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 


-- 
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