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Adaptive conformational sampling based on replicas

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Abstract

Computer simulations of biomolecules such as molecular dynamics simulations are limited by the time scale of conformational rearrangements. Several sampling techniques are available to search the multi-minima free energy landscape but most efficient, time-dependent methods do generally not produce a canonical ensemble. A sampling algorithm based on a self-regulating ladder of searching copies in the dihedral subspace is developped in this paper. The learning process using short- and long-term memory functions allows an efficient search in phase space while combining a deterministic dynamics and stochastic swaps with the searching copies conserves a canonical limit. The sampling efficiency and accuracy are indicated by comparing the ansatz with conventional molecular dynamics and replica exchange simulations.

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Authors and Affiliations

  1. Institute of Mathematics, Ecole Polytechnique Fédérale de Lausanne (EPFL), MATHGEOM, LCVMM, Station 8, MAC1 615, 1015, Lausanne, Switzerland

    Jeremy Curuksu

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  1. Jeremy Curuksu
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Correspondence to Jeremy Curuksu.

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Curuksu, J. Adaptive conformational sampling based on replicas. J. Math. Biol. 64, 917–931 (2012). https://doi.org/10.1007/s00285-011-0432-6

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  • DOI: https://doi.org/10.1007/s00285-011-0432-6

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