Hi everyone,
I’m working on a dimeric protein–ligand system in GROMACS, but during the simulation, the two monomers start drifting apart. I want to maintain the natural dimeric structure throughout the simulation.
I’ve already tried standard equilibration steps (energy minimization, NVT, and NPT), but even during the production MD, the monomers slowly separate.
Could anyone please suggest the best practices for handling dimeric proteins in such simulations?