Gromacs

Molecular Dynamics Simulations

    Table of contents
    1. 1. Books
    2. 2. Types / Ensembles
    3. 3. Resources

    Molecular dynamics (MD) is computer simulation with atoms and/or molecules interacting using some basic laws of physics.

    The GROMACS manual provides a good general introduction to this area, as well as specific material for use with GROMACS. The first few chapters are mandatory reading for anybody wishing to use GROMACS and not waste time.

    • Introduction to molecular modeling (slides,video)] - theoretical framework, modeling levels, limitations and possibilities, systems and methods (Erik Lindahl).
    • Introduction to molecular dynamics simulations (slides,video) - (Bert de Groot, Phil Biggin).
    • Introduction to Molecular Dynamics.

     

     

    Books

    There a several text books around:

    Good introductory books are:

    • A. Leach (2001) Molecular Modeling: Principles and Applications.
    • T. Schlick (2002) Molecular Modeling and Simulation

    With programming background:

    • D. Rapaport (1996) The Art of Molecular Dynamics Simulation
    • D. Frenkel, B. Smith (2001) Understanding Molecular Simulation

    More from the physicist's view:

    • M. Allen, D. Tildesley (1989) Computer simulation of liquids
    • H.J.C. Berendsen (2007) Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics

     

     

    Types / Ensembles

    • NVE - number of particles (N), system volume (V) and energy (E) are constant / conserved.
    • NVT - number of particles (N), system volume (V) and temperature (T) are constant / conserved. (See thermostats for more on "constant" temperature).
    • NPT - number of particles (N), system pressure (P) and temperature (T) are constant / conserved. (See pressure coupling for more on "constant" pressure).

     

    Resources

    • Beyond MD: stochastic methods. Mesoscopic approaches (slides,video) - (H.J.C. Berendsen).
    Page last modified 21:11, 28 Dec 2010 by JLemkul?