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On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics

Authors

  • Tetsuya Morishita,

    Corresponding author
    1. CREST-JST, Kawaguchi, Saitama, Japan
    2. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
    • Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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  • Satoru G. Itoh,

    1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
    2. Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
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  • Hisashi Okumura,

    1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
    2. Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
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  • Masuhiro Mikami

    1. Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
    2. CREST-JST, Kawaguchi, Saitama, Japan
    Current affiliation:
    1. Global Leader Carrier Development Network, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan. E-mail: t-morishita@aist.go.jp

Abstract

Mean-force dynamics (MFD), which is a fictitious dynamics for a set of collective variables on a potential of mean-force, is a powerful algorithm to efficiently explore free-energy landscapes. Recently, we have introduced logarithmic MFD (LogMFD) (Morishita et al., Phys. Rev. E 2012, 85, 066702) which overcomes difficulties encounterd in free-energy calculations using standard approaches such as thermodynamic integration. Here, we present a guide to implementing LogMFD calculations paying attention to the practical issues in choosing the parameters in LogMFD. A primary focus is given to the effect of the parameters on the accuracy of the reconstructed free-energy profiles. A recipe for reducing the errors due to energy dissipation is presented. We also demonstrate that multidimensional free-energy landscapes can be reconstructed on-the-fly using LogMFD, which cannot be accomplished using any other free-energy calculation techniques. © 2013 Wiley Periodicals, Inc.

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