Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.
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7 January 2011
Research Article|
January 07 2011
Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances
Joseph A. Morrone;
Joseph A. Morrone
a)
1Department of Chemistry,
Columbia University
, New York, New York 10027, USA
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Thomas E. Markland;
Thomas E. Markland
a)
1Department of Chemistry,
Columbia University
, New York, New York 10027, USA
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Michele Ceriotti;
Michele Ceriotti
2
Computational Science
, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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B. J. Berne
B. J. Berne
b)
1Department of Chemistry,
Columbia University
, New York, New York 10027, USA
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Joseph A. Morrone
1,a)
Thomas E. Markland
1,a)
Michele Ceriotti
2
B. J. Berne
1,b)
1Department of Chemistry,
Columbia University
, New York, New York 10027, USA
2
Computational Science
, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
a)
These authors contributed equally to this work.
b)
Electronic mail: [email protected].
J. Chem. Phys. 134, 014103 (2011)
Article history
Received:
August 30 2010
Accepted:
October 30 2010
Citation
Joseph A. Morrone, Thomas E. Markland, Michele Ceriotti, B. J. Berne; Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances. J. Chem. Phys. 7 January 2011; 134 (1): 014103. https://doi.org/10.1063/1.3518369
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