Dear gromacs users,
I am running a simulation for a ligand translocation vertically through a membrane protein. I prepared the system in charmm-gui and in the mdp files I used tc-coupling groups = protein membrane ligand solvent, maybe I should have used ligand together with the protein as the ligand contains only 140 atoms. The COM motion removal groups I used = protein_membrane solv_lig, as I checked that for interfacial systems it is better to use separate groups for membrane and solvent as their phases may drift apart due opposite direction of diffusion. Since the ligand is initially unbound and out in water and then it follows a vertical pathway along the z-direction for diffusion, I used lig com motion removal group separately. I did not get any LINCS error during the equilibration or production run or warning about possible collisions. However, in some previous threads I see that maybe the ligand can be coupled to the protein together as a com motion separation group. Is there any strong or visible effect of this com motion removal groups settings in the mdp file? Any help would be much appreciated.