This is the repository of core scripts to set up Molecular Dynamics (MD) simulations detailed in the manuscript "Chromatin Network Retards Nucleoli Coalescence" (bioRxiv).

• The first step is to set up the MD simulator Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), which is an open-source computational package for MD simulation. The standard LAMMPS package (tarball) can be downloaded here and following the doc of LAMMPS instructions to build the LAMMPS directory. We have been using the version lammps-17Nov16, on which our custom modifications were built.

• After downloading the standard LAMMPS package, copy our custom modifications in ./src/lammps/ to the directory /LAMMPS/src/ of the downloaded package and compile.

  • Note that the GCC compiler needs to be installed beforehand and an environment of OpenMPI is needed to compile the parallel version of LAMMPS.
  • On a "normal" desktop computer, the typical install time including download and compile steps is ~ 5 to 10 minutes.

• After the compilation of LAMMPS, direct the binary file in run.py (line 11) and execute run.py to simulate the trajectory in ./sim/run00/. Additional independent simulations can be performed by changing the run index in run.py (line 17) and re-execute the code.

• An example simulated trajectory is provided here.