[gmx-users] MD simulation stops without any error/warning message

[Michele Pellegrino]

Hi,


today I was running a MD simulation and it stopped without any error/warning message.

It just stopped: the md.log file reported everything till the last time step, and no information on the nature of the termination can be found in the standard output and the standard error.

I tried to restart the simulation using the last checkpoint but I got the error message:

-------------------------------------------------------
Program:     gmx mdrun, version 2019.4
Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)

Fatal error:
Failed to lock: md.log. Already running simulation?

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
So, I double-checked if the simulation was still running in the background (and exponentially slowed down, for some reason) or if I accidentally stopped the process in background (without killing it, though): no trace of the process to be found.
I run gmx energy with the default ener.edr file to see if it stopped because of some unphysical values for the temperature or the total energy, but everything seems to have stayed bounded.
It is actually the second time I find myself in this situation: is there another way to what find out could have gone wrong?


Thank you.


Cheers,

Michele