GROMACS version: 2023.3
GROMACS modification: Yes
I’m hoping to confirm that some membrane simulations have reached equilibration, and I was hoping to use RMSD, but I can’t find any resources on how to use this as an effective tool for equilibration. Should I be comparing my final production run to the last equilibrated frame, or is there a different approach to take?
So far, it looks like simulations are equilibrated based on gmx energy (checked potential, total energy, temperature, and pressure), but the box-x and box-y values don’t seem to reach a plateau when I check previous files (I can only see that it looks roughly average with the final output file). Any advice on how to confirm equilibration (or just check it!) with RMSD would be much appreciated- thank you!
There’s no guarantee your RMSD will ever stabilize. Having a stable temperature, pressure, and box size is a good prerequisite for initial equilibration, i.e. before you start production. But if your system’s RMSD keeps going up, it can mean many things - perhaps the initial model is badly prepared, or it’s evolving into a different stable state, which can reflect normal dynamic equilibrium, differences in physicochemical conditions, errors of the force field, errors in protonation states/PTMs and so on.
In the end, it’s a question of what the underlying process is that drives the increase in RMSD. You might have flexible elements that are perfectly allowed to move around, you might have experimental constraints on how much things should wiggle, and so on - it’s a case-by-case investigation.