hanatok / apoa1-benchmark Goto Github PK

nstlist in apoa1_nvt.mdp is set to 400, this is a little too large.
I test it in Gromacs/2019.5 version with 2 nodes (32 cores per node), it failed to run.
The error is:

There is no domain decomposition for 56 ranks that is compatible with the
given box and a minimum cell size of 2.9275 nm.

since 8 ranks are assigned to PME calculations.
I fixed this by changing nstlist from 400 to 40.

the margin is set to 8, which give a warning:
Warning: MARGIN IS UNUSUALLY LARGE AND WILL LOWER PERFORMANCE
I change it to 0, and the performance is doubled.
I also checked the parameter in official package as find in https://www.ks.uiuc.edu/Research/namd/utilities/.
They also have a margin of 0, though the force field is Charmm22.