cg_high_res_chromatin_setup

Setup scripts for high-resolution chromatin model in https://doi.org/10.1038/s41467-021-23090-3.

1. first look at https://github.com/CollepardoLab/CollepardoLab_Chromatin_Model.

2. This repo contains the python script to make the initial nucleosome structure and the lammps script to replicate it into a fiber.

3. setup.sh contains the steps (bash setup.sh):

• create a single nucleosome:

  python creation.py
  

  change the value of NRL in creation.py to set the nucleosome NRL. this creates nucl.txt - the lammps data file. And in.nucl - the first part of the lammps input script.

• setup the replication settings:

  python replicate_dna_seq.py $N > replicate_settings.txt
  cp new_DNA_sequence.txt DNA_sequence.txt
  

  where $N is the number of nucleosomes in the fiber

• make the input script with the run settings in run_settings.txt

  cat in.nucl run_settings.txt > run.in
  

• run the simulation:

  ./lmp -in run.in
  

The prodecure uses the lammps fix drag to pull the DNA linkers, it then uses replicate to create more nucleosomes, finally it uses create_bonds to join the nucleosomes together.