I’m trying to determine the position fluctuation correlation of a lipid molecule in relation to another lipid. Any option in gromacs that lets its user oscillate COM of a molecule back and forth along a reaction coordinate at a certain frequency?
No, we do not have time depend pull forces, except for a linear distance increase.
But I would think that if you want to measure corrections, you precisely do not want to put in an oscillating force, as you will then always get oscillating corrections, because you put those in. It would seem to me that you want to compute a position or velocity correlation function is an equilibrium simulation.