Not writing to output file for long simulation

User discussions
1

GROMACS version:5.1.4
GROMACS modification: No

Recently, we updated the ubuntu server version and reinstalled the gromacs-5.1.4. The small run simulations < 20ns finished successfully. The longer simulations >100ns are having issue to finish successfully. The top command shows that the gmx is running, but its not writing the md.log or .trr or edr files. The output file is not updated after around 76 ns for recently 100ns simulations.

I am having same issue with gromacs-2023 also. We have installed Ubuntu 22.04.2 server.

Is this a installation issue ? How to resolve this issue ?

Thanks,

Nilesh

2

Did similar runs finish before the operating system update?

You have not gotten any warnings on the stderr or in the log file?

The only case where we have seen such a thing happen is when the system suddenly gets unstable and one or more atoms jump very far away in a single step, which leads to an extremely long looping in the PBC code.