[gmx-users] Test if Trajectories are Independent

Johnny Lu johnny.lu128 at gmail.com
Thu Jan 22 21:11:37 CET 2015


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

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.

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