# Molecular Dynamics Simulation Resources

## Books

- [Understanding Molecular Simulation: From Algorithms to Applications](https://www.sciencedirect.com/book/9780122673511/understanding-molecular-simulation) by Daan Frenkel and Berend Smit
- [Computer Simulation of Liquids](https://academic.oup.com/book/27866) by Michael P. Allen and Dominic J. Tildesley
- [Statistical Mechanics: Theory and Molecular Simulation](https://global.oup.com/academic/product/statistical-mechanics-theory-and-molecular-simulation-9780198825562?cc=fr&lang=en&) by Mark Tuckerman
- [Molecular Modeling and Simulation: An Interdisciplinary Guide](https://link.springer.com/book/10.1007/978-1-4419-6351-2) by Tamar Schlick
- [Molecular Dynamics Simulation: Elementary Methods by J. M. Haile](https://www.wiley.com/en-us/Molecular+Dynamics+Simulation%3A+Elementary+Methods-p-9780471184393)
- [Soft Matter: Concepts, Phenomena, and Applications](https://softmatterbook.online/soft-matter-community/)

## General Resources

- KITP Program:
  - [Physical Principles Shaping Biomolecular Condensates](https://www.kitp.ucsb.edu/activities/biomol25)
  - [The Physics of Elastic Films: from Biological Membranes to Extreme Mechanics](https://online.kitp.ucsb.edu/online/films21/)
  - [Topics: Biomolecular Simulation Group Christine Peter, MPIPR & KITP](https://online.kitp.ucsb.edu//online/multiscale12/peter/)

- Boulder Summer School:
  - [2024: Self-Organizing Matter: From Inanimate to the Animate](https://boulderschool.yale.edu/2024/boulder-school-2024)
  - [2015: Soft Matter In and Out of Equilibrium](https://boulderschool.yale.edu/2015/boulder-school-2015)
  - [2012: Polymers in Soft and Biological Matter](https://boulderschool.yale.edu/2012/boulder-school-2012)
- Les Houches School of Physics:
  - [Soft Interfaces: Lecture Notes of the Les Houches Summer school: Volume 98, July 2012](https://doi.org/10.1093/oso/9780198789352.001.0001)
  - [From Molecules to Living Organisms : an Interplay between Biology and Physics : Lecture Notes of the Les Houches School of Physics (2016)](https://global.oup.com/academic/product/from-molecules-to-living-organisms-an-interplay-between-biology-and-physics-9780198752950?lang=en&cc=fr)
  - [Active Matter and Nonequilibrium Statistical Physics Lecture Notes of the Les Houches Summer School: Volume 112, 2018](https://global.oup.com/academic/product/active-matter-and-nonequilibrium-statistical-physics-9780192858313?lang=en&cc=fr)
- [LAMMPS Tutorials](https://lammpstutorials.github.io/index.html) by Simon Gravelle from LiPhy, UGA, CNRS, France.
- [Practical LAMMPS](https://www.lammps.org/tutorials.html) 

## Journals

- [Living Journal of Computational Molecular Science](https://livecomsjournal.org/)


## Online Repositories

- [LAMMPS](https://www.lammps.org/)
- [GROMACS](https://www.gromacs.org/)
- [OpenMM](https://openmm.org/)
- [ESPResSo](https://espressomd.org/wordpress/)
- [hoomdblue](https://glotzerlab.engin.umich.edu/hoomd-blue/)
- [NAMD](https://www.ks.uiuc.edu/Research/namd/)
- [OVITO](https://ovito.org/)
- [VMD](https://www.ks.uiuc.edu/Research/vmd/)