Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Table of Contents

Overview
System requirements
File description
How to run

Overview

The repository consists of scripts and codes used to study the scale dependent properties of chromatin. We use open source LAMMPS package to simulate chromatin polymer at nucleosome level. Then the custom c codes are used to compute coarse-grained properties of the chromatin polymer from an ensemble of configurations.

System requirements

• LAMMPS is an open source software. To see system requirements for LAMMPS click here.
• The analysis codes were tested on a Linux system (Ubuntu), but codes should work on MacOS or Windows system with corresponding C-compiler.
• The gcc compiler with math library was used to compile the analysis codes.

File description

• run.in - Script file for LAMMPS
• conf.dat - Initial input file with polymer configuration and information about extra chromatin contacts
• pos.xyz - Demo output position data file from simulation
• com_pos.c - Analysis code to find center of mass positions of CG beads
• cg_analysis.c - Uses the center of mass file obtained from com_pos.c to measure coarse-graining properties

How to run

• Refer LAMMPS documentation for installation. Run LAMMPS using command (make sure that the configuration file conf.dat is present in the same directory)

  ./lmp_serial <run.in

• Compile and run com_pos.c using

  gcc com_pos.c -lm
  ./a.out

• Compile and run cg_analysis.c using

  gcc cg_analysis.c -lm
  ./a.out

Expected output: The simulation generates single position trajectory file. The analysis codes compute average values and distributions of radius of gyration, bond length, and bond angle.

Typical installation for LAMMPS software is around 30 minutes. The simulation run for a single sample trajectory takes around 20 to 30 minutes. Analysis codes for single trajectory take less than a minute.