Gromacs

Beginners

    Table of contents
    1. 1. Resources

    For those just starting out with GROMACS and / or Molecular Dynamics Simulations it can be very daunting. It is highly recommended that the various and extensive documenation that has been made available for GROMACS is read first, plus papers published in the area of interest.

     

    Resources

    • GROMACS Manual - very detailed document that can also act as a very good introduction for MDS in general.
    • Flow Chart - simple flow chart of a typical GROMACS MD run of a protein in a box of water.
    • GROMACS Flowsheet - flowsheet of the general procedure for performing a molecular dynamic simulation using GROMACS. Shows linkage between files required and generated in each step and general command lines used.
    • Introduction to Molecular Dynamics.
    • Molecular dynamics simulations and GROMACS introduction (slides,video) - force fields, integrators, control of temperature and pressure (Berk Hess).
    • Introduction to modelling. From quantum to classical mechanics (slides,video) - (H.J.C. Berendsen).
    • Molecular dynamics simulations. Methods and applications (slides,video) - (H.J.C. Berendsen).
    Page last modified 10:15, 23 Mar 2011 by rossen