Carla Jamous wrote:
Hi everyone,
I concatenated many trajectories with trjcat and didn't have any problem.
But when I did trjconv, I had this warning:
WARNING: Incomplete frame: nr 6077 time 12154
so I tried to do gmxcheck on my concatenated .xtc and got :
Reading frame 0 time 0.000
# Atoms 192409
Precision 0.001 (nm)
Reading frame 6000 time 12000.001
WARNING: Incomplete frame: nr 6077 time 12154
Item #frames Timestep (ps)
Step 6077 2
Time 6077 2
Lambda 0
Coords 6077 2
Velocities 0
Forces 0
Box 6077 2
please can anyone tell me what might be the problem, knowing that when I
gmxcheck the file .xtc that contains this frame, I don't get a warning.
Two possibilities:
1. trjcat corrupted the frame when trying to write the full trajectory
2. The original non-concatenated trajectory is corrupted and trjcat passed over
the problem, while trjconv cannot.
Check the original (non-concatenated) trajectories to assess their integrity.
If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted
frame(s), which may mean re-running from a point prior to the corruption.
-Justin
Thank you,
Carla
--
========================================
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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