On the truncation of long-range electrostatic interactions in DNA.

[1]  P. P. Ewald.  Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[2]  G. Fasman,et al.  Handbook of biochemistry and molecular biology. Nucleic acids - v. 1 - 3. ed. , 1975 .

[3]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[4]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[5]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

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

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

[8]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

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

[10]  H. Berendsen,et al.  Simulations of Proteins in Water a , 1986, Annals of the New York Academy of Sciences.

[11]  J. Mccammon,et al.  Dynamics of Proteins and Nucleic Acids , 2018 .

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

[13]  B. Brooks,et al.  The effects of truncating long‐range forces on protein dynamics , 1989, Proteins.

[14]  Wilfred F. van Gunsteren,et al.  Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .

[15]  S. Harvey.  Treatment of electrostatic effects in macromolecular modeling , 1989, Proteins.

[16]  H. Berendsen,et al.  COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .

[17]  Shoshana J. Wodak,et al.  Computer simulations of liquid water: treatment of long-range interactions , 1990 .

[18]  Bernard Pettitt,et al.  Peptides in ionic solutions: A comparison of the Ewald and switching function techniques , 1991 .

[19]  H. Schreiber,et al.  Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work , 1992 .

[20]  P A Kollman,et al.  Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor , 1992, Protein science : a publication of the Protein Society.

[21]  O. Steinhauser,et al.  Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method. , 1992, Journal of molecular biology.

[22]  O. Steinhauser,et al.  Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. , 1992, Biochemistry.

[23]  Minoru Saito,et al.  Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions , 1992 .

[24]  T. Darden,et al.  The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods , 1993 .

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

[26]  Peter A. Kollman,et al.  Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation , 1993, J. Comput. Chem..

[27]  D. Nguyen,et al.  On achieving better than 1-A accuracy in a simulation of a large protein: Streptomyces griseus protease A. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Bernard R. Brooks,et al.  New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..

[29]  Minoru Saito,et al.  Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation , 1994 .

[30]  G. C. Levy,et al.  13C-NMR relaxation in three DNA oligonucleotide duplexes: model-free analysis of internal and overall motion. , 1994, Biochemistry.

[31]  L. Nilsson,et al.  High-pressure molecular dynamics of a nucleic acid fragment , 1994 .

[32]  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 .

[33]  L. Nilsson,et al.  Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. , 1995, Biophysical journal.

[34]  L. Nilsson,et al.  NMR RELAXATION TIMES, DYNAMICS, AND HYDRATION OF A NUCLEIC ACID FRAGMENT FROM MOLECULAR DYNAMICS SIMULATIONS , 1995 .

[35]  T. Darden,et al.  Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC , 1995 .

[36]  Eric Westhof,et al.  MULTIPLE MOLECULAR DYNAMICS SIMULATIONS OF THE ANTICODON LOOP OF TRNAASP IN AQUEOUS SOLUTION WITH COUNTERIONS , 1995 .

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

[38]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[39]  T. Darden,et al.  Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics , 1995 .

[40]  B. Montgomery Pettitt,et al.  Efficient Ewald electrostatic calculations for large systems , 1995 .

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

[42]  B. Montgomery Pettitt,et al.  Nanosecond Dynamics and Structure of a Model DNA Triple Helix in Saltwater Solution , 1995 .

[43]  B. Montgomery Pettitt,et al.  B to A Transition of DNA on the Nanosecond Time Scale , 1996 .

[44]  E. Westhof,et al.  H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations. , 1996, Biophysical journal.

[45]  R. Osman,et al.  Computational Simulations of DNA Distortions by a cis,syn-Cyclobutane Thymine Dimer Lesion† , 1996 .

[46]  J M Rosenberg,et al.  Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases. , 1996, Journal of molecular biology.

[47]  Lennart Nilsson,et al.  Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2 , 1996 .

[48]  P A Kollman,et al.  Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. , 1996, Journal of molecular biology.

[49]  B. Brooks,et al.  Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water , 1996 .

[50]  Jim Glosli,et al.  Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems , 1996 .

[51]  L. Nilsson,et al.  Internal mobility of the ologonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations , 1996 .

[52]  B. Montgomery Pettitt,et al.  Ewald artifacts in liquid state molecular dynamics simulations , 1996 .

[53]  R. Ornstein,et al.  Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using AMBER 4.1 and particle-mesh Ewald method. , 1997, Journal of biomolecular structure & dynamics.

[54]  Lee G. Pedersen,et al.  Long-range electrostatic effects in biomolecular simulations , 1997 .

[55]  H Weinstein,et al.  Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein. , 1997, Biophysical journal.

[56]  Insight via simulations: Publishing results and methods , 1997 .

[57]  D. Beveridge,et al.  A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. , 1997, Biophysical journal.

[58]  Alexander D. MacKerell.  Influence of Magnesium Ions on Duplex DNA Structural, Dynamic, and Solvation Properties , 1997 .

[59]  M. Orozco,et al.  Molecular Dynamics Simulations of the d(T·A·T) Triple Helix , 1997 .

[60]  R. Ornstein,et al.  Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method. , 1997, Biophysical journal.

[61]  B. Pettitt,et al.  Experiment vs force fields: DNA conformation from molecular dynamics simulations , 1997 .

[62]  J M Rosenberg,et al.  Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration. , 1997, Journal of molecular biology.

[63]  P. Kollman,et al.  Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition , 1997 .

[64]  Christian Holm,et al.  How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .

[65]  Bernard R. Brooks,et al.  Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution , 1998 .

[66]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[67]  D. Langley,et al.  Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. , 1998, Journal of biomolecular structure & dynamics.

[68]  M Feig,et al.  Structural equilibrium of DNA represented with different force fields. , 1998, Biophysical journal.

[69]  L. Nilsson,et al.  Solvent influence on base stacking. , 1998, Biophysical journal.

[70]  J. Gready,et al.  Molecular dynamics simulations of human prion protein: importance of correct treatment of electrostatic interactions. , 1999, Biochemistry.

[71]  T. Darden,et al.  Molecular dynamics simulations of biomolecules: long-range electrostatic effects. , 1999, Annual review of biophysics and biomolecular structure.

[72]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[73]  T Darden,et al.  New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. , 1999, Structure.

[74]  Yuto Komeiji,et al.  Molecular Dynamics Simulation of the Hin-Recombinase—DNA Complex , 1999 .

[75]  B. Pettitt,et al.  Sodium and chlorine ions as part of the DNA solvation shell. , 1999, Biophysical journal.

[76]  R. Ornstein,et al.  Molecular dynamics simulations of a protein-protein dimer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model. , 1999, Journal of biomolecular structure & dynamics.

[77]  L. Li,et al.  Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment. , 2000, Biophysical journal.

[78]  Christian Holm,et al.  How to Mesh up Ewald Sums , 2000 .

[79]  J. Mccammon,et al.  Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation , 2000 .

[80]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[81]  Eric Westhof,et al.  Molecular Dynamics: Simulations of Nucleic Acids , 2002 .