Two chains and two ligands were put for simulation in the water system, and a conformation with low free energy was obtained through calculation, in which a ligand was attached to two bodies and bonded by hydrogen bonds. I hoped to put this conformation into another system (alcohol-water system) for the next simulation. After running, the structure found that the conformation was dispersed during running.
Is there any way to keep this conformation together and not separate during the simulation?
Thanks.