achattaraj / condensatemerger

Simulation scripts used in the study "Separation of sticker-spacer energetics governs the coalescence of metastable biomolecular condensates"

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.

• 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)

• N200_clustering contains files regarding the metadynamics simulation of 200 chains becoming one large cluster

• TwoCluster_setup contains python scripts to a copy a cluster that serves as the initial condition for two-cluster fusion simulation

• 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

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