[gmx-users] Interpretation of MSD

[Pandya, Akash]

Hi all,

I performed Mean Square Deviation for my ligand molecules in x, y, z directions in order to obtain the diffusion coefficients. From my understanding, the square root of the highest MSD value should be significant enough to interpret that the ligand molecules have in fact moved enough during the course of the simulation. This may seem like an ambiguous question, but what would you deem a suitable value for MSD, for diffusion coefficients to be appropriate to measure?

Many thanks,

Akash