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
========================================
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