NucleosomeLinker

Source Code for the paper 'Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly'

We are delighted to share our model for chromatin phase separation and analysis scripts with the community. Please use it freely and cite our paper: preprint https://www.biorxiv.org/content/10.1101/2024.12.23.627571v1.

For questions, contact Julia Maristany in mjm261@cam.ac.uk

System requirements

• Linux operating system
• C++ compiler with MPI support (e.g., Intel, GCC, or Cray)
• MPI library (e.g., Intel MPI, OpenMPI)
• Python 3.6+ for analysis scripts
• Optional: Ovito, VMD, or PyMOL for trajectory visualization

Tested on:

• CSD3 Cluster with Intel 2017 compilers
• ARCHER HPC (Cray system with GNU and Cray compilers)
• Sulis Tier 2 HPC

Installation Guide

Our code build on the custom LAMMPS code from the multiscale model repository: https://github.com/CollepardoLab/CollepardoLab_Chromatin_Model

To install:

1. Clone the LAMMPS repository and follow build instructions in the README.md there - ensure you are installing the most up-to-date version.
2. Ensure the resulting binary is named lmp_DNA_mpi or lmp (or adapt following scripts and code accordingly).
3. Typical install time is about 10 minutes on a standard HPC node, a bit more on a desktop.

Demo

To run a demo for a slab system:

1. Move to the "Demo" directory

2. Run with lammps, on at least 16 cores

mpirun -np 16 ./lmp_DNA_mpi -in in.run

It will produce two LAMMPS trajectory files, "dna.dump" and "cores.dump", a reduced version without the DNA. These can be viewed in Ovito (https://www.ovito.org/), VMD or Pymol. The expected runtime, for a few frames of simulation, is on the order of minutes on most modern 16-core CPUs.

Full simulation setup

These simulations can be used to reproduce the results from this paper. To fully reproduce phase diagrams one needs to vary the parameters E1 and A in the input script. The correct mapping can be found in salt mapping scripts if desired, but this mapping is automated via bash scripting. More details on how to reproduce results are found in the Simulation folder.

Analysis

Under Analysis, all custom Python scripts to analyze the trajectories can be found.

License

This project is licensed under GNU General Public License v3.0.