GROMACS version: GROMACS/2021-foss-2020b
GROMACS modification: Yes (HPC installation)
Maybe my previous question was too long, I’ll keep it short.
When attempting domain decomposition for my simulation, the log file shows:
"Initial maximum distances in bonded interactions:
two-body bonded interactions: 0.429 nm, LJ-14, atoms 1837 1845
multi-body bonded interactions: 0.488 nm, CMAP Dih., atoms 440 449
Minimum cell size due to bonded interactions: 0.537 nm”
But the simulatoin never starts, as I get the fatal error:
“1196 of the 49025 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.835804 nm) or the two-body cut-off distance (1.59575 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck”
I don’t understand how this can happen if the initial maximum distances are well below the cut-off distances. Could someone explain how I should interpret this error?
Log file: step5_6.log - Google Drive
Basic system info: protein-ligand complex in a rhombic dodecahedral box of ~409nm³, (box-X, box-Y, box-Z) ~= (8.33, 8.33, 5.89)nm. The system consists of 41672 atoms.