https://github.com/ankhoa1212/molecular-dynamics-simulation
This project uses LAMMPS to simulate molecular dynamics
https://github.com/ankhoa1212/molecular-dynamics-simulation
bash-scripting cplusplus docker lammps molecular-dynamics-simulation python3
Last synced: 4 months ago
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This project uses LAMMPS to simulate molecular dynamics
- Host: GitHub
- URL: https://github.com/ankhoa1212/molecular-dynamics-simulation
- Owner: ankhoa1212
- Created: 2025-02-27T22:35:23.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-07-25T22:28:10.000Z (11 months ago)
- Last Synced: 2025-07-26T05:57:04.323Z (11 months ago)
- Topics: bash-scripting, cplusplus, docker, lammps, molecular-dynamics-simulation, python3
- Language: Python
- Homepage:
- Size: 43.6 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# molecular-dynamics-simulation
This project uses LAMMPS to simulate molecular dynamics.
## Linux Setup
[Install](https://docs.lammps.org/Install.html) and [Build](https://docs.lammps.org/Build.html) 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](https://www.docker.com/get-started/) Docker.
Pull docker image:
```
docker pull ankhoa1212/lammps-simulations:latest
```
## Resources
- [LAMMPS Manual](https://docs.lammps.org/Manual.html)
- [Installation](https://docs.lammps.org/Install.html)
- [Examples](https://docs.lammps.org/Examples.html)
- [Processing Tools](https://docs.lammps.org/Tools.html)
- [Library Interfaces](https://docs.lammps.org/Library.html)
- [Modifying and extending LAMMPS](https://docs.lammps.org/Modify.html)
- [Light-Responsive Assembly](https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02301)
- [Molecular Dynamics Simulation of Active Particles Video](https://www.youtube.com/watch?v=wsM2kUB6XU4&ab_channel=SoftMatterLab)
- [Molecular Dynamics Simulation of Active Particles (Brownian Motion)](https://arxiv.org/abs/2102.10399)
- [OVITO (for Visualization)](https://www.ovito.org/)