Thematic school on soft nanosciences

This repository contains simple simulations of water and ethanol that can be used with the open-source software LAMMPS.

25 septembre 2023, UGA, Grenoble

1 - Install LAMMPS

Install the open-source code LAMMPS following the instructions of this page. On linux system, the following command usually does the trick:

sudo apt-get install lammps

2 - Clone this repository

Download the content of this repository, or clone it using

https://github.com/simongravelle/thematic-school-soft-nanosciences-2023.git

3 - Run a simulation

Choosing any of the 3 simulations located in the molecular-dynamics-scripts/ folder, run lammps by executing the input script in a terminal:

lmp -in input.lammps

Here, the input.lammps file contains all the commands that control the simulation. Each command is described in depth on the LAMMPS website.

If you are interested in learning molecular simulations from scratch, I recommend that you follow the beginner tutorials here.

4 - Visualise the trajectory

Each simulation will produce a trajectory file named "dump.lammpstrj", containing the positions of the molecules over time. You can open it using VMD,

vmd dump.lammpstrj

Contact

Please don't hesitate to send me an email at simon.gravelle at univ-grenoble-alpes.fr if you encounter difficulties when installing LAMMPS of VMD.

Acknowledgments

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101065060.