How to analyse a BIT_FED run - martaenciso/BIT_FED GitHub Wiki

BIT_FED will automatically stop when it finds no more allowed bins to spawn from. Then, the BIT_FED_run.sh script will clean up temporary files and leave the rest intact. Meaningful information can be extracted using the script BIT_FED_analysis.sh, which is described here.

The analysis starts building the reconstructed trajectories, which will be used throughout this analysis and then stored in the main folder of the BIT_FED run. These trajectories can be later analysed as any conventional molecular dynamics run.

Then, the script identifies the optimal lag time by fitting the average RMSD values at different intervals to the Hill equation (see original papers for details). It first converts the reconstructed dcd trajectory files into temporary xyz files by means of convert_dcd_to_xyz.f90, which are then analysed using rmsd_analysis.f90. Averages and then calculated and fed into a GNUplot script, that generates a rmsd_vs_time.ps plot as well as the optimal lag time.

The count matrices needed for the free energy calculations are then built using the program calculate_count_matrix.f90 and stored in a file called counts.dat, that is used as input for the free energy utility.