Essential readings on molecular modeling for serious professionals

Review Articles

• General MD methodologies
• JCC Special Issue on MD Packages (Vol. 26 Issue 16);
• Brooks et al., 2009 (PMID: 19444816; the updated CHARMM paper);
• Hess et al., J. Chem. Theo. Comput. (2008) (GROMACS 4 paper);
• Tuckerman and Martyna, J. Phys. Chem. B (2000);
• Schlick et al., J. Comput. Phys. (1999);
• Scheraga et al., 2007 (PMID: 17034338);
• Force Fields (No, they were not created by God.)
• MacKerell, 2004 (PMID: 15264253): CHARMM-central review with broader pespective
• Ponder and Case, 2003 (PMID: 14631816): general overview of empirical force fields
• Lazaridis and Karplus, 2000 (PMID: 10753811): with some discussion on statistical potentials.
• Implicit Solvent
• Simonson and Roux, 1999 (PMID: 17030302)
• Bashford and Case, 2000 (PMID: 11031278)
• Feig and Brooks, 2004 (PMID: 15093837); an update, Chen et al., 2008 (PMID: 18304802);
• Free Energy Methods
• Case and Brooks, Chem. Rev. (1993);
• Kollman, Chem. Rev. (1993);
• Kumar et al., J. Comput. Chem. (1992,1995) (the original WHAM paper and multidimensional extension);
• Gilson et al., Biophys. J. (1997) (almost all to be known about binding affinity calculations);
• Allen et al., 2006 (PMID 16500984: ; ion channel PMF)

• "Understanding Molecular Simulations", by Frankel and Smit
• "Computer Simulations of Liquids", by Allen and Tildesley
• "Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics", by Brooks, Karplus and Pettitt
• "Statistical Mechanics", by McQuarrie
• "Introduction to Modern Statistical Mechanics", by David Chandler

• CHARMM
• Amber
• NAMD/VMD
• Gromacs