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Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

J. Chem. Phys. 129, 014105 (2008); doi:10.1063/1.2949815

Published 3 July 2008

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Lianqing Zheng1 and Wei Yang1,2
1Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
2Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang–Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping. ©2008 American Institute of Physics
History: Received 11 February 2008; accepted 3 June 2008; published 3 July 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/014105/1
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KEYWORDS and PACS

Keywords
PACS
  • 02.70.Ns
    Molecular dynamics and particle methods
  • 02.60.-x
    Numerical approximation and analysis
  • 02.50.-r
    Probability theory, stochastic processes, and statistics
  • 05.20.-y
    Classical statistical mechanics
  • 05.70.Ce
    Thermodynamic functions and equations of state
  • YEAR: 2008

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ISSN:
0021-9606 (print)   1089-7690 (online)
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