A Coarse-Grained Simulation Model for Colloidal Self-Assembly via Explicit Mobile Binders (SUBMITTED)

(Gaurav Mitra, Chuan Chang, Angus McMullen, Daniela Puchall, Jasna Brujic, and Glen M. Hocky)

This repository contains the python framework for performing MD simulations to study self-assembly of droplets with mobile binders.

We have three main folders/directories for the 3 types of simulations we perform:

1.dimer_trimer 2.lattice_of_droplets 3.folding

The dynamic binding/unbinding code is in the folder dybond.

NOTE: Singularity files have to be present in the folder ./dybond/singularity for successful compilation of the dybond plugin.

NOTE: SLURM should be available as the default workload manager in order to be able to run and use this workflow

DOWNLOAD THE SINGULARITY FILES FROM HERE:

https://drive.google.com/file/d/15vH54mzLhiscVWF9_P6IRNhIRQntYn3Q/view?usp=sharing

After downloading the singularity files (present as a zip file in the link above), unzip them and save the files individually in the folder dybond/singularity/ before running anything else.

Each folder for the 3 types of simulations contains an analysis folder and a simulation_setup folder. In addition, there is a folder named main_python_scripts_simulationsetup outside of all these folders which contains the 5 main .py scripts which can read in parameters from yaml files, set up the system and run the MD simulations by calling the Dynamic Bond Updater.

Detailed instructions for setting up simulations and performing specific analyses (and generating the figures discussed in the main text / SI) is provided in the README files of these sub-folders.