Journal of Mathematical Biology

, Volume 64, Issue 6, pp 917–931 | Cite as

Adaptive conformational sampling based on replicas

Article

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.

Keywords

Adaptive sampling Convergence of molecular dynamics Replica exchange Dihedral angles 

Mathematics Subject Classification (2000)

82B05 82C05 

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Institute of MathematicsEcole Polytechnique Fédérale de Lausanne (EPFL), MATHGEOM, LCVMMLausanneSwitzerland

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