Gmx velacc - Process killed after reading the final frame

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

My aim is to compute the diffusion coefficient of methanol in a zeolite using the velocity autocorrelation function.

I run the following command:

gmx velacc -f traj.trr -nonormalize -n index.ndx -s H-ZSM-5-61MeOH.tpr -o vac_H-ZSM-5-MeOH.xvg

I then select the group corresponding to the methanol molecules, and I receive the following output:

trr version: GMX_trn_file (single precision)
Reading frame 428000 time 59920.000
Killed

The simulation time is 60 ns, so all frames got read before the process was killed.
I ran

gmx check -f traj.trr

and it produced the following output:

Checking file traj.trr
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 3711
Reading frame 428000 time 59920.000

Item #frames Timestep (ps)
Step 428572 0.14
Time 428572 0.14
Lambda 428572 0.14
Coords 428572 0.14
Velocities 428572 0.14
Forces 0
Box 428572 0.14

Does anyone have some idea on how I should proceed to troubleshoot the issue?

Thank you very much in advance for your help.

Regards,
Torstein

2

Hello,

you could try to stop reading before the final frame, in case it is partially corrupt. Use -e 59900 to read up until 59.9 ns.

Regards,
Petter