Identification of the optimal lagtime - martaenciso/BIT_FED GitHub Wiki

---OLD VERSION--- Once a simulation has finished and long trajectories have been properly reconstructed, the construction of the Markov State Model matrix (MSM matrix) needs to define a proper lagtime.

The BIT_FED method does this through the rmsd.sh script, which is based on a method by Schreiner and co-workers.

This script converts a reconstructed simulation trajectory (in dcd format) into a XYZ format trajectory. Then, it loops over different possible lagtimes l and calls the FORTRAN program rmsd_analysis.f90 for each of them. This program calculates the RMSD (root mean standard deviation) between pairs of configurations separated by that l lagtime and stores them in the file lagtime_l.dat.

Then, it plots these results using a gnuplot script and fits the data to the Hill equation (see the original paper for details). This fitting gives us τ, which will be used as optimal lagtime.

---NEW VERSION--- Use of time-structure indipendent component analysis (TICA)