Error when rerunning a trajectory

User discussions
1

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!

Anna

2

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

3

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

4

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.

5

Hi all,
Is there any solution?

6

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