1CPN model documentation

1CPN Website: https://lequieu.github.io/1cpn-model/

1CPN GitHub: https://github.com/lequieu/1cpn-model

This is the documentation for the 1CPN model implementation in LAMMPS. If you haven’t read the 1CPN paper yet, please read it before reading this documentation:

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

If you’re just looking to install and compile 1CPN with LAMMPS, begin with the “quickstart” guide.

If you have any issues with 1CPN, please let us know on the our GitHub issues page page. Please don’t hesitate to reach out, we’re grateful for your interest in 1CPN and would love to help you get up and running.

Also, we welcome pull requests and so if you’d like to contribute to any part of the 1CPN project please let us know.

• Quick Start
  • Getting 1CPN and compiling with LAMMPS
  • Running your first simulation
  • Analyzing the Simulation
• 1CPN Implementation in Lammps
  • Linking 1CPN with LAMMPS
  • 1CPN Performance across many processors
  • Custom 1CPN Potentials
  • Maintaing Compatability with LAMMPS
• Initialization
• Vizualization of 1CPN
  • Option 1: Basic VMD
  • Option 2. Enhanced VMD (recommended)
  • Option 3. Blender
• Analysis of 1CPN Simulations
• Corrections of the 1CPN Paper
  • Updates on Fig. 6 of 1CPN Paper
  • \(\varepsilon_{0, H4cut}\) in TABLE. S3 of 1CPN paper