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KPrepFunction

Introduction to KPrepFunction

This is likely the biggest file in KPrep and contains a lot of scripts useful for model manipulation. The detail and scope covered is large and all functionality is not covered here. For a full list of functions, open the KPrepFunctions.py file and read the header and comments. This space is reserved for special instructions or information about certain algorithms within this script.

We note that KPrepFunctions contains scripts that are outside the scope of "Prep" and are used for post-processing.

List of Algorithms and the Necessary Information

mbarNC_screenDCD_to_nc

This function post-processes .dcd files from LAMMPS RepX simulations and gets everything ready for MBAR analysis with native contact analysis. Essential for this to function is MDAnalysis. The MDAnalysis package requires special attention to be installed on FSL, see "MDAnalysis in KPrep"

This script is necessary because LAMMPS RepX simulations print data according to screen. Instead of swapping coordinates during RepX, LAMMPS swaps temperatures to streamline simulation. However, MBAR requires box data where box "temperature" is constant (thus coordinates would have been swapped). To read the .dcd files outputted from LAMMPS, MDAnalysis is necessary. Trajectories are then swapped into the appropriate boxes.

IMPORTANT: This script assumes that the .dcd files print ("dump") trajectories at every "swapping" attempt. Thus the frequency of each trajectory "dump" must match the "tempering swap attempt" parameter defined in the "temper" command.