This repository is part of the study - "Separation of sticker-spacer energetics governs the coalescence of metastable biomolecular condensates". It contains files used to setup simulations and analyze the data.

The repository is organized in order of the simulation pipeline:

1. InitialCondition_setup contains codes to create two types of polymer chains in a template based manner (using MolTemplate) and fill in 200 chains in a simulation box (using packmol). The script create_InitCoor.sh executes these codes to create initial data file to start LAMMPS simulations.

2. N200_clustering contains files regarding the metadynamics simulation of 200 chains becoming one large cluster. The README file contains detailed descriptions about the simulation setup and execution.

3. TwoClusterSetUp_v2.ipynb is a python notebook with code that copies the cluster created by the initial simulations (N200_clustering), and creates datafile containing two identical side-by-side clusters in a proportionally larger simulation box. This datafile is then used as initial conditions for two-cluster fusion simulation.

4. Two_cluster_fusion_S10N03kT contains files that exemplify metadynamics simulation of two-cluster fusion at a given pair of energy parameters (Es = 10kT, Ens = 0.3kT). Similar simulations are performed for a range of parameter combinations.

5. ClusterProperty contains python scripts used to analyze the biophysical properties of the cluster.

• How to run LAMMPS
• bond_style harmonic/shift/cut (Note: This bond style can only be used if LAMMPS was built with the EXTRA-MOLECULE package)
• bond formation in LAMMPS. The modified version (bond/create/random) can be found in this article