GROMACS version: version 2020.5
I am running coarse-grained simulations on a system which has 124966 atoms and consists of DNA, pore and a bilayer. It is not the first time I am running MD simulations on this system so I am getting an error which is new for me. I created the system and minimization and equilibration steps seemed all fine when I compared these steps with older sytems that I created using on an older GROMACS version with an older computer. However I am getting a segmentation fault constantly when I want to run the production step. When I looked into the .log file I saw initial temperature as infinite although it is given as 320 K.
For information, when I run other simulations I am not getting this kind of error. I have the same DNA-pore-bilayer system with a different DNA orientation at the entrance of the pore and it works fine on my computer. Finally, when I run this system with which I am getting this segmentation fault on the clusters we use in the laboratory, it works also fine… Any help is appreciated!!