Error when rerunning a trajectory

GROMACS version: 2016.1
GROMACS modification: No

Hello everyone,
I’m triying to rerun a trajectory in order to calculate interaction energy between groups.
Please tell me if I did something wrong

I added in the mdp file (md_umbrella.mdp) this line:
energygrps = BEN DUM OTL

then I created the new tpr file (prova-rer.tpr)
gmx grompp -f md_umbrella.mdp -c npt.gro -t npt.cpt -o prova-rer.tpr -n index.ndx

npt.gro and npt.cpt are the files I used for running the simulation I want to rerun, which is called md.*

I then used the new tpr for rerunning the trajectory md.trr:
gmx mdrun -rerun md.trr -deffnm prova-rer

The problem is that I got this error:
Fatal error:
Rerun trajectory frame step 2500000 time 5000.000000 does not contain a box,
while pbc is used

I can’t understand it, because obviously I have a box…

I don’t know if you have some suggestions…

Thank you a lot!


The error suggests a corruption in the file. What does gmx check tell you about the .trr file?

thank you for your reply!
Here’s what I obtain:

Command line:
gmx check -f md.trr

Checking file md.trr
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000

Atoms 36591

Last frame 500 time 5000.000
WARNING: Incomplete header: nr 501 time 5000

Item #frames Timestep (ps)
Step 501 10
Time 501 10
Lambda 501 10
Coords 0
Velocities 501 10
Forces 501 10
Box 501 10

As I suspected, the final frame of your trajectory file is corrupted. Probably your file system had an issue when mdrun was writing to it and you have an incomplete frame.

Hi all,
Is there any solution?

Have the same problem.
gmx check -f traj.trr

Checking file traj.trr
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000

Atoms 28788

Last frame 2000 time 100000.000

Item #frames Timestep (ps)
Step 2001 50
Time 2001 50
Lambda 2001 50
Coords 0
Velocities 2001 50
Forces 0
Box 2001 50