Literature

Newtonian mechanics

Integrators in The Art of Computational Science

Molecular Dynamics, Structure Optimization, Forces calculations in Guanghua Gao thesis.

Bekker, Hendrik. Molecular dynamics simulation methods revised.

Monte Carlo

Hess, Berk. Stochastic concepts in molecular simulation.

Alexander P. Lyubartsev and Aatto Laaksonen. Inverse Monte Carlo.

Molecular Modeling

Edward J. Maginn. Molecular Modeling and Theory.

David Lai Gwai Cheung Ph.D Thesis.
Structures and Properties of Liquid Crystals and Related Molecules from Computer Simulation.

Miscellaneous

Richard F.W. Bader Theory of Atoms in Molecules.

Course on protein structure and comparative modeling.

CMBI homology modelling course

Principles of Protein Structure Using the Internet.
       Section 7 - Overview of Molecular Forces
       Section 8 - Protein Secondary Structure

Software for


Ascalaph


Freeware