Adaptive conformational sampling based on replicas

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.


Published in:
Journal Of Mathematical Biology, 64, 917-931
Year:
2012
Keywords:
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 Record created 2012-06-01, last modified 2018-03-17


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