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PROTCLUS

  1. PROTCLUS.sh
  • Measures protein clustering vs time in a given MD simulation (XTC format of gromacs) and plots it using matplotlib;
  • Provides a protein clustering score; irrespective of atomistic/ coarse-grained resolution.
  • This shell script contains USAGE, INTRO, REQUIREMENTS, VARIABLES, RUN, and PLOT sections. Explore using a text editor for details.
  1. PROTCLUS_avg.py
  • For multiple simulation replicates, execute the shell script separately. This python script is to extract the average from all simulations and plot.