[gmx-users] Test if Trajectories are Independent

[Johnny Lu]

Hi.

Is there a good way to test if a set of trajectories are independent from
each other?

I was thinking about

a) show that the initial structures of the trajectories are sufficiently
different.

b) calculate rmsd between corresponding frames of two trajectories.
If the trajectories are independent, the rmsd should be random and possibly
have an autocorrelation with a fast decay to zero.

I'm working with three 100 ns trajectories of alanine tripeptide.

Thank you again.