GROMACS version:2022.0
GROMACS modification: No
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Hi,
I have a water box with a small molecule, and I want to calculate its diffusion coefficient. I conducted a 150 ns long MD simulation at 298 K and obtained the following MSD graph.
At the end of the simulation, the graph showed non-linear behavior. Would considering the initial region (e.g., 2-20 ns) of the graph be a correct way to calculate the diffusion coefficient of the molecule?