Construction of the count matrix - martaenciso/BIT_FED GitHub Wiki

A count matrix stores the information about the number of times that a configuration in bin i en in in j after a certain time called lag time. This matrix is needed to build the transition matrix, key to build the Markov State Model that will produce the free energy results of BIT_FED.

The count matrix is calculated within the BIT_FED_analysis.sh script, described here. It uses the reconstructed trajectory files and an optimal lag time.