General

A number of good review-type papers can be found in the following two journal issues

• Acc. Chem. Res., 2002, 35(6), produced for the 25th anniversary of the first protein simulation 
• J. Comp. Chem., 2005, 26(16), which describes a number of the main MD packages

Applications

Membranes

• Diffusion in membranes, calculated and NMR rotational lifetimes: J. Chem. Phys. 122, 244715 (2005)
• Coarse Grained MD, insertion of a trans-membrane pore: Biophys J. 2005 88 3083
• Free energy pathways for ion channels: J. Phys. Chem. B 2005, 109, 19516  

Proteins

• HPPK enzyme with HP substrate: J. Mol. Struct.: THEOCHEM 2005, 731, 23
• MD of bovine rhodopsin: J Mol Model 2005, 12, 49
• Langevin dynamics of  bovine pancreatic tripsin inhibitor: Proteins: Struct. Func. Bioinf., 2005, 60, 464
• Simulated protein folding, folding@home: J. Chem. Phys. 2006, 124, 164902

DNA 

• Stacking free energies in DNA: Chem. Eur. J. 2005, 11, 4340
• MD of 136 different tetranucleotide sequences: Biophys. J. 2005, 89, 3721

Methods

• A detailed overview of the Ewald Summation for Coulombic Interactions in a Periodic Supercell.