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

LAMMPS simulations used during the 2023 thematic school
https://github.com/simongravelle/thematic-school-soft-nanosciences-2023

lammps molecular-dynamics school

Last synced: 8 days ago
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LAMMPS simulations used during the 2023 thematic school

• Host: GitHub
• URL: https://github.com/simongravelle/thematic-school-soft-nanosciences-2023
• Owner: simongravelle
• License: gpl-3.0
• Created: 2023-09-24T15:12:53.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-08-19T12:05:59.000Z (5 months ago)
• Last Synced: 2024-11-08T16:43:04.522Z (2 months ago)
• Topics: lammps, molecular-dynamics, school
• Homepage:
• Size: 10.3 MB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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[![DOI](https://zenodo.org/badge/695899700.svg)](https://zenodo.org/doi/10.5281/zenodo.13341960)

[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

# 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](https://docs.lammps.org/Install.html). On linux system,

the following command usually does the trick:

```bash

sudo apt-get install lammps

```

## 2 - Clone this repository

Download the content of this repository, or clone it 

using 

```bash

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/](molecular-dynamics-scripts/) folder, run lammps by executing

the input script in a terminal:

```bash

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](https://docs.lammps.org/Manual.html). 

If you are interested in learning molecular simulations from scratch, I recommend that you follow the [beginner tutorials here](https://lammpstutorials.github.io/).

## 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](https://www.ks.uiuc.edu/Research/vmd/),

```bash

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.