Hi everyone,
I have a simulation of protein in water for 100 ns and all the necessary trjconv is done.
I wanted to calculate the diffusion coefficient of the water around certain residues using MSD curve slopes.
I notices that, when I change the MSD calculation window (200ps, 500 ps, 1000 ps) the slopes getting steeper and diffusion coefficients increased.
| 200ps | 500ps | 1000ps |
|---|---|---|
| 1.47E-05 | 1.64E-05 | 1.77E-05 |
My question is, what is the protocol to use the ideal/best MSD calculation window?
FYI: I used same region with linear regression for each calculation