R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. 15 Phys., 103(21):9444--9459, December 1 1995. Home/Search Document Details and Download
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A Test Set for Molecular Dynamics Algorithms - Barth, Leimkuhler, Reich (2002) (Correct)
....they vary significantly. MTS methods have been developed which share the abstract geometric properties (and also favorable energy conservation) with the Verlet method [84,86] For solvated systems, fast summation methods have been successfully combined with multiple timestep integration methods [87,88]. Variations of the method given in (3.20) include employing switching functions such as (3.21) to intermolecular (water water) distances rather than interatomic distances or using switching functions to split the potential, rather than the force. Procacci and Berne point out that these schemes ....
R. Zhou and B.J. Berne, A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems, J. Chem. Phys., 103 (1995), pp. 9444--9459
Framework Design, Parallelization and Force Computation in.. - Matthey (Correct)
....different MD applications [11, 48, 73] and is especially suited for parallelization [93, 95, 96, 123] However, optimized FMM codes tend to be rather elaborate. More importantly, they do not conserve energy during MD simulations unless enforcing unusual high accuracy, e.g. 12th order multi poles [10, 128]. Typically, the electrostatic problem comes with usually small distributions of mono pole moments that cause self cancellation; positive and negative charges are roughly canceled. 3.6 Other fast electrostatic methods There exist many fast electrostatic methods and implementations. Typically, ....
R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. Phys., 103(21):9444--9459, 1995.
Masking resonance artifacts in force-splitting methods for.. - Sandu, Schlick (1998) (6 citations) (Correct)
....temporal division can be exploited by using small timesteps ( Delta ) to resolve the rapidly varying vibrational modes and larger time intervals ( Deltat) to update the costly long range forces. In the early to mid 1990s, these approaches were further developed and applied to biomolecular dynamics [6, 7, 8, 9]. Much of these developments relied on the 4 ADRIAN SANDU AND TAMAR SCHLICK rigorous and general factorization formalism (disparate timescales, masses, etc. of the r RESPA method based on the Trotter factorization [6] a special case of which is the Verlet I method [7] These methods are ....
R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. Phys., 103:9444--9459, 1995.
Verlet-I/r-RESPA/Impulse Is Limited by Nonlinear Instability - Ma, Izaguirre, Skeel (Correct)
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R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. 15 Phys., 103(21):9444--9459, December 1 1995.
Targeted Mollified Impulse - A Multiscale Stochastic.. - Ma, Izaguirre (2003) (Correct)
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R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. Phys., 103(21):9444--9459, 1995.
Novel Multiscale Algorithms for Molecular Dynamics - Ma (2003) (Correct)
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R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Chem. Phys., 103(21):9444--9459, December 1 1995.
Ego - An Efficient Molecular Dynamics Program And Its.. - Eichinger, Heller.. (2000) (Correct)
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R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Phys. Chem., 103:9444-- 9459, 1995.
Conformational Dynamics Simulations of Proteins - Eichinger, Heymann, Heller.. (Correct)
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R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Phys. Chem., 103:9444--9459, 1995.
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