Dear gromacs users,
I am running a coarse-grained md simulation with martini forcefield in gromacs. I am getting an error: “1 of the 8420 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (1.169 nm)
or the two-body cut-off distance (1.169 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck”
In some online martini sources I see it is recommended to use the option -rdd 1.4 flag in the mdrun command. I checked that this rdd flag refers to domain decomposition distance, however, I don’t fully understand the meaning of this term. However, using this flag, I don’t see the domain-decomposition errors anymore. Does this term anyway affect the system dynamics or energy or this is just a software related and performance based flag that does not interfere with the simulation outcome? Any help would be much appreciated, thank you.