GROMACS version: 2024
GROMACS modification: Yes/No
Hi everyone,
Relevantly new to GROMACS
I’m working on molecular dynamics simulations using GROMACS and was wondering if there are any established methods to extract kinetic parameters (even from 3rd party plugins) such as:
Michaelis-Menten constants (Km, kcat)
Catalytic Efficiency (Kcat/Km)
Binding/unbinding rates (kon, koff)
From my MD trajectories, I have binding/unbinding events, free energy calculations (MM/GBSA), and interaction data.
Does anyone have experience with this or recommendations for tools/papers that discuss extracting kinetic rates from MD simulations?