Force fields for classical molecular dynamics.

[1]  Benjamin Lindner,et al.  Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. , 2009, Journal of chemical theory and computation.

[2]  R. Pastor,et al.  Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers. , 2009, The journal of physical chemistry. B.

[3]  P. Hünenberger,et al.  Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics , 2008 .

[4]  David L Mobley,et al.  Accurate and efficient corrections for missing dispersion interactions in molecular simulations. , 2007, The journal of physical chemistry. B.

[5]  Gary S Grest,et al.  Application of Ewald summations to long-range dispersion forces. , 2007, The Journal of chemical physics.

[6]  Arieh Warshel,et al.  Modeling electrostatic effects in proteins. , 2006, Biochimica et biophysica acta.

[7]  P. Kollman,et al.  Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.

[8]  Christian Kandt,et al.  Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins , 2006, Journal of physics. Condensed matter : an Institute of Physics journal.

[9]  Wilfred F van Gunsteren,et al.  Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.

[10]  Mika A. Kastenholz,et al.  Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation. , 2006, The Journal of chemical physics.

[11]  Mika A. Kastenholz,et al.  Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids. , 2006, The Journal of chemical physics.

[12]  Carlos J. V. Simões,et al.  Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides , 2006 .

[13]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[14]  Alexander D. MacKerell.  Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..

[15]  B. Roux,et al.  Energetics of ion conduction through the gramicidin channel , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Siewert J. Marrink,et al.  Methodological issues in lipid bilayer simulations , 2003 .

[17]  W. L. Jorgensen.  Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water , 2002 .

[18]  W. V. van Gunsteren,et al.  Comparison of different schemes to treat long‐range electrostatic interactions in molecular dynamics simulations of a protein crystal , 2001, Proteins.

[19]  M. Levitt.  The birth of computational structural biology , 2001, Nature Structural Biology.

[20]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[21]  Wilfred F. van Gunsteren,et al.  Validation of molecular dynamics simulation , 1998 .

[22]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[23]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[24]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[25]  K. Esselink.  A comparison of algorithms for long-range interactions , 1995 .

[26]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[27]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[28]  P. Kollman,et al.  Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins , 1995 .

[29]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[30]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[31]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[32]  William L. Jorgensen,et al.  Optimized intermolecular potential functions for liquid hydrocarbons , 1984 .

[33]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[34]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[35]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[36]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[37]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[38]  A. Warshel,et al.  Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules , 1968 .

[39]  Mika A. Kastenholz,et al.  Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods , 2004 .

[40]  T. Schlick.  Molecular Modeling and Simulation: An Interdisciplinary Guide , 2003 .

[41]  J. Ponder,et al.  Force fields for protein simulations. , 2003, Advances in protein chemistry.

[42]  B. Hess.  Determining the shear viscosity of model liquids from molecular dynamics simulations , 2002 .

[43]  A. Leach.  Molecular Modelling: Principles and Applications , 1996 .

[44]  B. Montgomery Pettitt,et al.  Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids , 1985 .