Task 11 - Molecular Dynamics Simulation

Intro

Several experimental techniques, such as X-ray crystallography, NMR and spectroscopy, can provide information on the structure and dynamics of biological macromolecules, in our case proteins. However, experimental methods are often time-consuming and do not provide a complete picture of the dynamic properties of proteins. Structural bioinformatics can complement experimental methods. Molecular dynamics (MD) simulations provide invaluable insight into protein dynamics considering the full range of harmonic and anharmonic motions at the atomic level.

Several different force fields and simulation packages exist. The first

To learn about MD: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/

Slides to introductory talk: File:MD presentation.pdf

Gallery that show MD simulations under different level of details: http://www.ks.uiuc.edu/Gallery/

Gromacs is installed here:

/opt/SS12-Practical/gromacs/bin/