Hello, everyone!
I want to simulate the interaction between peptides and vesicle. I have used packmol to build an all-atom vesicle. Now I want to simulate the interaction between peptides and vesicles. How should I set comm-grps in the mdp file?
At present, I still set peptide and vesicle as a group and the rest as a group according to my previous habit, and the comm-mode is set to Angular.
Thanks！
You should not specify separate groups for COM motion removal. Leave it set to the default (System). The correct mode is Linear. Angular is only for non-periodic or gas-phase systems. It is not appropriate for the condensed phase.