Error computing diffusion coefficient

User discussions
1

GROMACS version: 2018.1
GROMACS modification: No
I am trying to compute the diffusion coefficient using the gmx msd command.

echo 1 | gmx msd -f mol_A.nojump.mol.xtc -s em.tpr -o mol_A_msd.xvg

After initiating the command, I got the following
Run 1

Reading frame 56000 time 560200.000 Killed

Run 2

Reading frame 88000 time 880200.000 srun: error: hpc005: task 0: Killed

What could be wrong? I check the trajectory using the gmx check command and the trajectory has the complete timesteps

2

Hi - you likely ran out of memory, MSD calculations take a lot of memory. Try skipping some frames with the -trestart option.

3

Thanks for your suggestion. It worked!