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 ?
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.
I’m getting the same issue. there is a continuous pattern. im trying to runa 100 ns simulation and the log file stop updating after al most 35 ns. so I have to restart my simulation 2 times to get 100 ns completed. My system doesnot have gpu and although i downloaded and installed gromacs 2024 but after installation when i check the version of gromacs it says 2021.
I don’t know what can be the cause of this issue, except for the extremely long PBC loop I mentioned before. That has been removed in the 2024 release. So I suggest to use GROMACS 2024, or even better: 2025.
It sound impossible that you get GROMACS 2021 after installing 2024, except when you already had a version installed somewhere else.