Molecular Dynamics Simulation Resources

Books

• Understanding Molecular Simulation: From Algorithms to Applications by Daan Frenkel and Berend Smit

• Computer Simulation of Liquids by Michael P. Allen and Dominic J. Tildesley

• Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman

• Molecular Modeling and Simulation: An Interdisciplinary Guide by Tamar Schlick

• Molecular Dynamics Simulation: Elementary Methods by J. M. Haile

• Soft Matter: Concepts, Phenomena, and Applications

General Resources

• KITP Program:

  • Physical Principles Shaping Biomolecular Condensates

  • The Physics of Elastic Films: from Biological Membranes to Extreme Mechanics

  • Topics: Biomolecular Simulation Group Christine Peter, MPIPR & KITP

• Boulder Summer School:

  • 2024: Self-Organizing Matter: From Inanimate to the Animate

  • 2015: Soft Matter In and Out of Equilibrium

  • 2012: Polymers in Soft and Biological Matter

• Les Houches School of Physics:

  • Soft Interfaces: Lecture Notes of the Les Houches Summer school: Volume 98, July 2012

  • From Molecules to Living Organisms : an Interplay between Biology and Physics : Lecture Notes of the Les Houches School of Physics (2016)

  • Active Matter and Nonequilibrium Statistical Physics Lecture Notes of the Les Houches Summer School: Volume 112, 2018

• LAMMPS Tutorials by Simon Gravelle from LiPhy, UGA, CNRS, France.

• Practical LAMMPS

Journals

• Living Journal of Computational Molecular Science

Online Repositories

• LAMMPS

• GROMACS

• OpenMM

• ESPResSo

• hoomdblue

• NAMD

• OVITO

• VMD