1CPN Model

Welcome to the LAMMPS implementation of the 1CPN model of chromatin.

The first thing you'll want to do is familiarize youself with the 1CPN manuscript:

Lequieu, Cordoba, Moller, de Pablo "1CPN: A coarse-grained multi-scale model of chromatin" (2019) J. Chem. Phys. 150, 215102

Getting Started

The best way to get started with 1CPN is go to the documentation, and follow the "Quick Start" tutorial. This section will explain everything you need to know to use 1CPN model including:

• Compiling LAMMPS with 1CPN
• Generating an initial 1CPN configuration and input files
• Running a Simple Simulation
• Vizualizing and Analyzing Results

What's Included

• src/

  • lammps/ - Core of 1CPN model, as implemented into LAMMPS
  • viz/ - Tools for vizualizing 1CPN in VMD
  • analysis/ - Tools for analyzing a 1CPN trajectory
  • include/ - Includes for .cpp code

• init/ - Scripts to generate initial configuration for 1CPN
• inputs/ - LAMMPS input scripts for 1CPN model
• doc/ - Documentation written in .rst and Sphinx (for building, see below)
• test/ - Testing Code
• utils/ - Utilities for 1CPN model
• bin/ - Directory where built binary files are written

Issues?

If you run into any issues don't hesitate to reach out. We'd love to help you get up and running.