GROMACS version: 2020.4
GROMACS modification: No
Using virtual sites for hydrogen atoms I am able to use 5 fs time step if using GPU (single MPI rank). However, I get domain decomposition error when trying to run the simulation on HPC node with 128 cores:
There is no domain decomposition for 96 ranks that is compatible with the
given box and a minimum cell size of 1.49875 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
Look in the log file for details on the domain decomposition”
The simulation works on the CPU node with 4 fs time step and lincs-order = 4. With lincs-order = 6 I get the same domain decomposition error.
Without virtual sites and using 2 fs time step the simulation runs fluently on multiple CPU nodes without any issues at all.
Would it be possible to use the 5 fs time step when running on the CPU nodes?