Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems

The Journal of Chemical Physics ◽

10.1063/1.1385159 ◽

2001 ◽

Vol 115 (5) ◽

pp. 2348-2358 ◽

Author(s):

Ruhong Zhou ◽

Edward Harder ◽

Huafeng Xu ◽

B. J. Berne

Keyword(s):

Multiple Time ◽

Step Method ◽

Time Step ◽

Biomolecular Systems ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

Time Step Method

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Folding Energy Landscape of Two Model Peptides : Brownian Dynamics Simulation with Multiple Time Step Method Approach

Seibutsu Butsuri ◽

10.2142/biophys.43.s57_4 ◽

2003 ◽

Vol 43 (supplement) ◽

pp. S57

Author(s):

Tadashi Ando ◽

Toshiyuki Meguro ◽

Ichiro Yamato

Keyword(s):

Brownian Dynamics ◽

Dynamics Simulation ◽

Multiple Time ◽

Folding Energy ◽

Brownian Dynamics Simulation ◽

Step Method ◽

Time Step ◽

Multiple Time Step ◽

Time Step Method ◽

Method Approach

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A multiple time-step method for molecular dynamics simulations of fluids of chain molecules

Journal of Computational Physics ◽

10.1016/0021-9991(84)90042-1 ◽

1984 ◽

Vol 53 (2) ◽

pp. 289-298 ◽

Author(s):

R.D Swindoll ◽

J.M Haile

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Multiple Time ◽

Step Method ◽

Time Step ◽

Chain Molecules ◽

Multiple Time Step ◽

Dynamics Simulations ◽

Time Step Method

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Corrigendum to “Acceleration of the canonical molecular dynamics simulation by the particle mesh Ewald method combined with the multiple time-step integrator algorithm”

Chemical Physics Letters ◽

10.1016/s0009-2614(99)01408-6 ◽

2000 ◽

Vol 317 (3-5) ◽

pp. 515 ◽

Author(s):

Masaaki Kawata ◽

Masuhiro Mikami

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

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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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Application of a Multiple Time Step Algorithm to Biomolecular Systems

The Journal of Physical Chemistry B ◽

10.1021/jp990231w ◽

1999 ◽

Vol 103 (25) ◽

pp. 5396-5405 ◽

Author(s):

Ailan Cheng ◽

Kenneth M. Merz

Keyword(s):

Multiple Time ◽

Time Step ◽

Biomolecular Systems ◽

Multiple Time Step ◽

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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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Acceleration of the canonical molecular dynamics simulation by the particle mesh Ewald method combined with the multiple time-step integrator algorithm

Chemical Physics Letters ◽

10.1016/s0009-2614(99)00930-6 ◽

1999 ◽

Vol 313 (1-2) ◽

pp. 261-266 ◽

Author(s):

Masaaki Kawata ◽

Masuhiro Mikami

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step ◽

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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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Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

Journal of Computational Chemistry ◽

10.1002/jcc.10196 ◽

2002 ◽

Vol 24 (1) ◽

pp. 77-88 ◽

Author(s):

Danny Barash ◽

Linjing Yang ◽

Xiaoliang Qian ◽

Tamar Schlick

Keyword(s):

Multiple Time ◽

Time Step ◽

Particle Mesh Ewald ◽

Multiple Time Step

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