Overview
System requirements
File description
How to run
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.
./lmp_serial <run.in
gcc com_pos.c -lm
./a.out
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.