Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

Keywords

Fading, Rayleigh fading, Signal-to-noise ratio (imaging), Energy (signal processing), Maximal-ratio combining

References

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Cited by

• Comparison of Replica-Permutation Molecular Dynamics Simulations with and without Detailed Balance ConditionHiroaki Nishizawa, Hisashi Okumura — 2015
• Length Dependence of Polyglycine Conformations in VacuumSatoru Itoh, Hisashi Okumura — 2011
• Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.Junichi Ono, Koji Ando — 2012
• Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm.Tetsuro Nagai, Takuya Takahashi — 2014
• Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics methodHisashi Okumura — 2012
• Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles.I. P. Omelyan, Andriy Kovalenko — 2011
• Generalized-ensemble algorithms for molecular dynamics simulationsSatoru Itoh, Hisashi Okumura, Yuko Okamoto — 2007
• Cutoff Effect in the Nosé–Poincaré and Nosé–Hoover ThermostatsTakeshi Sakaguchi, Hisashi Okumura — 2013
• Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.Satoru G. Itoh, Hisashi Okumura, Yuko Okamoto — 2009
• Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.Hisashi Okumura — 2008
• Aqua ions-graphene interfacial and confinement behavior: insights from isobaric-isothermal molecular dynamics.Ariel A. Chialvo, Peter T. Cummings — 2011
• Thermodynamic properties of methane/water interface predicted by molecular dynamics simulations.Ryuji Sakamaki, Amadeu K. Sum, Tetsu Narumi — 2011
• Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.Hisashi Okumura — 2011
• Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature AlgorithmsY. Mori, Yuko Okamoto — 2010
• Fast time-reversible algorithms for molecular dynamics of rigid-body systems.Yasuhiro Kajima, Miyabi Hiyama, Shūji Ogata — 2012
• Reversible structure transformation in ice nanocluster.Kengo Nishio, Masuhiro Mikami — 2009
• Multibaric–multithermal molecular dynamics simulation: generalized Nosé–Poincaré–Andersen methodHisashi Okumura, Yuko Okamoto — 2007
• Angular Momentum Form of Verlet Algorithm for Rigid Molecules(General)Miyabi Hiyama, Tomoyuki Kinjo, Shi-aki Hyodo — 2008
• Generalized-ensemble molecular dynamics and Monte Carlo algorithms beyond the limit of the multicanonical algorithmHisashi Okumura — 2010
• Manifold Correction Method for the Nosé–Hoover and Nosé–Poincaré Molecular Dynamics SimulationsHisashi Okumura, Satoru Itoh, Atsushi Ito — 2014

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