Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm
被引:13
作者:
Chen, Yunjie
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Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, Dept Chem, Chicago, IL 60637 USA
Chen, Yunjie
[1
]
Kale, Seyit
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Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, Dept Chem, Chicago, IL 60637 USA
Kale, Seyit
[1
]
Weare, Jonathan
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机构:
Univ Chicago, Dept Stat, Chicago, IL 60637 USA
Univ Chicago, James Franck Inst, Chicago, IL 60637 USAUniv Chicago, Dept Chem, Chicago, IL 60637 USA
Weare, Jonathan
[2
,3
]
Dinner, Aaron R.
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Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, Dept Chem, Chicago, IL 60637 USA
Dinner, Aaron R.
[1
]
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机构:
Roux, Benoit
[1
,4
,5
]
机构:
[1] Univ Chicago, Dept Chem, Chicago, IL 60637 USA
[2] Univ Chicago, Dept Stat, Chicago, IL 60637 USA
[3] Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
[4] Univ Chicago, Dept Biochem & Mol Biol, Chicago, IL 60637 USA
[5] Argonne Natl Lab, Ctr Nanomat, Argonne, IL 60439 USA
A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method.
机构:
Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
Sivak, David A.
;
Chodera, John D.
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机构:
Mem Sloan Kettering Canc Ctr, Computat Biol Program, New York, NY 10065 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
Chodera, John D.
;
Crooks, Gavin E.
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机构:
Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
机构:
Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
Sivak, David A.
;
Chodera, John D.
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h-index: 0
机构:
Mem Sloan Kettering Canc Ctr, Computat Biol Program, New York, NY 10065 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA
Chodera, John D.
;
Crooks, Gavin E.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USAUniv Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA