Forum:Books And Articles For Md Simulation Experiments And Analysis

Question

[aravind ramesh]

Please list useful books or research or review articles for conducting MD simulation Experiments, and analysis of the results. Books which include various methods and techniques used for understanding and analysis the results obtained after simulation. Thanks in advance.

Answer 1

[João Rodrigues]

Books:

1. Molecular Modelling: Principles and Applications by Andrew Leach
2. Understanding Molecular Simulation, Second Edition: From Algorithms to Applications by Frenkel and Smit

These two are enough I'd say to understand what's going on in a MD simulation and programs. They do not deal with a few recent advances, but the basic math and ideas are all there.

Historical Papers:

• Levitt M, Lifson S (1969) Refinement of protein conformations using a macromolecular energy minimization procedure. J Mol Biol 46:269–279. (First energy minimization of a protein structure) [ [PDF][3] ]
• Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253:694–698. (Folding simulation, pre-MD) [ [PDF][4] ]
• McCammon J, Gelin B, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590. (First MD simulation) [ [Nature][5] ]
• Levitt M, Sharon R (1988) Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci USA 85:7557. (First MD simulation in water) [ [PDF][6] ]

Other Papers:

• Shaw DE et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341–346. (1st millisecond simulation) [ [PDF][7] ]

Reviews:

• Scheraga HA, Khalili M, Liwo A (2007) Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58:57–83. [ [PDF][8] ]
• Guvench O, MacKerell A (2008) Comparison of protein force fields for molecular dynamics simulations. METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA- 443:63. [ [Pubmed][9] ]
• Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X (2011) Biomolecular modeling and simulation: a field coming of age. Quarterly Reviews of Biophysics 44:191–228. [ [PDF][10] ]

[João Rodrigues]

A quick question. Does anyone know why the post doesn't have the links for the papers showing? If I edit the post it previews fine but afterwards not anymore..