Molecular modelling, dynamics and design

Molecular dynamics

Introduction to molecular dynamics simulation

Video intro to molecular dynamics simulations Watch!

Wiki page: https://en.wikipedia.org/wiki/Molecular_dynamics

Geometry (energy) optimization is a typical feature of these software

Software:

Gromacs

Chimera molecular modelling software system. Nice

Delphi Electrostatic fields

Ascalaph designer and abalone. Tutorial

AMBER

http://proteopedia.org/wiki/index.php/Molecular_modeling_and_visualization_software

http://nanohub.org/

http://nanohub.org/resources/4540

https://en.wikipedia.org/wiki/Molecule_editor

https://en.wikipedia.org/wiki/List_of_software_for_Monte_Carlo_molecular_modeling

https://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling

https://en.wikipedia.org/wiki/List_of_software_for_nanostructures_modeling

http://www.ch.ic.ac.uk/local/organic/mod/software.html

Challenges in computer-aided molecule design