Rheoinformatic Colloids Simulation Setup Guide

Welcome to the Rheoinformatic colloids simulation team! 🎉

These files will guide you through everything you need to know to start running colloid simulations with HOOMD-blue for research in our group.

[Last Update: November 2023]

Before you Begin

If you are ordering or setting up a new computer:

• The System Setup folder contains information for choosing a laptop or other workstation, and steps for setting up a new MacOS computer before installing HOOMD-blue.

If you are new to programming:

• The Programming Resources folder contains some references that can help you get started the command line, VIM, Python, R, C++, Git/Github, and other skills that are useful for our work.

The remaining files will help you install HOOMD-blue and VMD and start running colloid simulations.

HPC Access, Installing Software, and Running Simulations

Follow these guides to get set up with the Discovery Research Cluster, HOOMD-blue, VMD, and other tools:

1. Accessing "Discovery" (Northeastern's HPC cluster)

2. An introduction to running HPC simulations

3. The HOOMD-blue Installation and Setup Guide

4. An introduction to running a basic DPD simulation with HOOMD-blue: Simulating waterDPD

5. The VMD Installation Guide

6. An introduction to Using VMD to qualitiatively check your simulation results.

7. The Analysis Guide for quantitatively checking your results.

8. An overview of simulating colloids with our modifications: Gelation and Shearing