GROMACS version: 2022
GROMACS modification: No
Fatal error:
DD cell 13 0 0 could only obtain 1356 of the 1357 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order.
I have 80 chains, each containing 40 carbon atoms. Initially, they are all extended. I run minimization followed by a short NVT simulation at 400 K. The simulation box is large. However, when I run NPT at 400 K, I encounter an error.
My guess is that you system is not sufficiently equilibrated/minimized. At what step does this happen? Do you get very high kinetic energy / temperatures?
Note that we would like to avoid that users gets such low-level errors, but sometimes this is difficult to avoid.
It happens during equilibration. After the NVT step, a large void appears in the simulation, causing a drastic reduction in box size, which leads to an error. Is there a way to remove the Coulombic force for a few timesteps?
Then I would simply increase tau_p (a lot), that will make the box shrink slower. This assumes that you are using the c-rescale barostat, which you should for equilibration.