README.md

backmapping

• Below are the files and a general overview of what they do
  • backpack (module)
    • mapanly.py - takes in the dataframes of coordinates/bonds/dihedrals etc and outputs the bond lengths/angles of each chain
    • mapback.py - all functions related to physically backmapping those course grained models
    • writepack.py - all functions regarding reading and writing lammps formatted coordinate files
  • backmap.py - run this to backmap a specified lammps configured coordinate file
  • default_configs.py - default lammps configs as a dictionary
  • speed_test.py - used to test the speed of the backmapping algorithm with changing monomer no
  • test.py - file for testing individual components

stuff to get done

• analysis package
  • need a series of functions to analyze the output of the backmapping workflow at each step
    • g(r)
    • dihedral angles
    • bond angles
• write_backmapping protocol
  • need to pattern out how the current bashmap.sh and in. files on talapas work and organize around that

hopes and dreams

• taking the analysis package and creating a sort of monte carlo style simulation where we can map how certain thermodynamic factors or other general parameters within lammps affect the structure
  • in less eloquent terms, i have a vague understanding of what a force field is, instead of learning how to effectively make one i would rather brute force my way to victory!
• one word, proteins
  • best way would be to just have a general program that can orient the specific amino acids in their given order
    • start with a large bead
      • easy
    • move on using the splitting method we normally do
      • easy
    • onece the full chain is there, split the backbone from the r as beads
      • maybe easy
    • finally atomize the backbone and sidechain
      • easy