molecular-dynamics-simulation

This project uses LAMMPS to simulate molecular dynamics.

Linux Setup

Install and Build LAMMPS.

Temporary Environment Variable Setup

Use the following to set up env variables in the commandline to run the lmp command (first navigate to the directory of the executable):

EXECUTABLE_DIR=$PWD

export PATH=$EXECUTABLE_DIR:$PATH

Bash Shell Environment Variable Setup

Add the following to the ~/.bashrc file (replace /path/to/dir with the path to the directory of the executable):

export PATH=/path/to/dir:$PATH

Setup Ovito

If on an old Linux Ubuntu version less than 22.04 that does not have qt.qpa.plugin 6.5.0 may need to install libxcb-cursor0

Docker Setup (Work in progress)

Install Docker.

Pull docker image:

docker pull ankhoa1212/lammps-simulations:latest

Resources

• LAMMPS Manual
  • Installation
  • Examples
  • Processing Tools
  • Library Interfaces
  • Modifying and extending LAMMPS
• Light-Responsive Assembly
• Molecular Dynamics Simulation of Active Particles Video
• Molecular Dynamics Simulation of Active Particles (Brownian Motion)
• OVITO (for Visualization)