Dimeric protein handling during simulation

User discussions
1

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?

2

Could you provide a full description of the system? Is there a specific reason that you’re certain the dimer is stable enough that they shouldn’t separate in simulation? Do the simulation conditions match the conditions you would expect the dimers to remain bound?