Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

Chemical Physics Letters ◽

10.1016/0009-2614(95)00845-u ◽

1995 ◽

Vol 243 (3-4) ◽

pp. 229-235 ◽

Author(s):

Hsing Lee ◽

Thomas Darden ◽

Lee Pedersen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Particle Mesh Ewald ◽

Dynamics Simulations

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Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

Journal of the American Chemical Society ◽

10.1021/ja00119a045 ◽

1995 ◽

Vol 117 (14) ◽

pp. 4193-4194 ◽

Author(s):

T. E. III Cheatham ◽

J. L. Miller ◽

T. Fox ◽

T. A. Darden ◽

P. A. Kollman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Biomolecular Systems ◽

Particle Mesh Ewald ◽

Ewald Method ◽

Dynamics Simulations

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Erratum: “Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations” [J. Chem. Phys. 116, 5971 (2002)]

The Journal of Chemical Physics ◽

10.1063/1.1487820 ◽

2002 ◽

Vol 117 (4) ◽

pp. 1927-1927

Author(s):

X. Qian ◽

T. Schlick

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Chem Phys ◽

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

Dynamics Simulations

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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Journal of Chemical Theory and Computation ◽

10.1021/ct400314y ◽

2013 ◽

Vol 9 (9) ◽

pp. 3878-3888 ◽

Cited By ~ 1296

Author(s):

Romelia Salomon-Ferrer ◽

Andreas W. Götz ◽

Duncan Poole ◽

Scott Le Grand ◽

Ross C. Walker

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Particle Mesh Ewald ◽

Explicit Solvent ◽

Dynamics Simulations

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Computationally efficient canonical molecular dynamics simulations by using a multiple time-step integrator algorithm combined with the particle mesh Ewald method and with the fast multipole method

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(200002)21:3<201::aid-jcc4>3.0.co;2-# ◽

2000 ◽

Vol 21 (3) ◽

pp. 201-217 ◽

Author(s):

Masaaki Kawata ◽

Masuhiro Mikami

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Fast Multipole Method ◽

Multiple Time ◽

Computationally Efficient ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

Ewald Method ◽

Dynamics Simulations

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Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.1389854 ◽

2001 ◽

Vol 115 (9) ◽

pp. 4003-4018 ◽

Author(s):

Paul F. Batcho ◽

David A. Case ◽

Tamar Schlick

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

Dynamics Simulations

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Molecular Dynamics Simulations of a Protein-Protein Dimer: Particle-Mesh Ewald Electrostatic Model Yields Far Superior Results to Standard Cutoff Model

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.1999.10508328 ◽

1999 ◽

Vol 16 (6) ◽

pp. 1205-1218 ◽

Author(s):

Osmar Norberto de Souza ◽

Rick L. Ornstein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Model ◽

Particle Mesh Ewald ◽

Protein Dimer ◽

Dynamics Simulations

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Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.1458542 ◽

2002 ◽

Vol 116 (14) ◽

pp. 5971-5983 ◽

Author(s):

Xiaoliang Qian ◽

Tamar Schlick

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

Dynamics Simulations

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An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations

Computer Physics Communications ◽

10.1016/j.cpc.2007.05.005 ◽

2007 ◽

Vol 177 (5) ◽

pp. 426-431 ◽

Author(s):

Kwang Jin Oh ◽

Yuefan Deng

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Parallel Implementation ◽

Particle Mesh Ewald ◽

Ewald Method ◽

Dynamics Simulations

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NMR Structure Refinement and Dynamics of the K+-[d(G3T4G3)]2 Quadruplex via Particle Mesh Ewald Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/s0006-3495(98)77585-x ◽

1998 ◽

Vol 75 (2) ◽

pp. 968-981 ◽

Author(s):

Gary D. Strahan ◽

Max A. Keniry ◽

Richard H. Shafer

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Nmr Structure ◽

Particle Mesh Ewald ◽

Dynamics Simulations

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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

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.1997.10508160 ◽

1997 ◽

Vol 14 (5) ◽

pp. 607-611 ◽

Author(s):

Osmar Norberto de Souza ◽

Rick L. Ornstein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sampling Time ◽

Particle Mesh Ewald ◽

Ewald Method ◽

Amber 4.1 ◽

Dynamics Simulations ◽

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