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LAMMPS code to simulate loop extrusion of DNA by SMC complexes

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LucasDooms/SMC_LAMMPS

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DNA Loop Extrusion by SMCCs in LAMMPS

Authors

Original code by Stefanos Nomidis (https://github.com/sknomidis/SMC_LAMMPS).
Modifications by Arwin Goossens.
All commits in this repository by Lucas Dooms.
Released under MIT license

How to run

  1. Define all parameters in "parameters"
  2. Run python run.py ..., provide the directory of the parameters file, use the -g flag to generate the required parameterfile and datafile.

examples:

  • python run.py 7nm_kleisin -g to generate and run
  • python run.py 7nm_kleisin -gpv to generate, run, post-process, and visualize
  • python run.py 7nm_kleisin -gvn to generate, run, and visualize while ignoring errors

help:
python run.py --help

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LAMMPS code to simulate loop extrusion of DNA by SMC complexes

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