title: Adaptive conformational sampling based on replicas.
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.
authors.affiliation: Institute of Mathematics, Ecole Polytechnique Fédérale de Lausanne-EPFL, MATHGEOM, LCVMM, Station 8, MAC1 615, 1015 Lausanne, Switzerland. jeremy.curuksu@epfl.ch
authors.forename: Jeremy
authors.initials: J
authors.lastname: Curuksu
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry
chemical_list: D009696:Nucleic Acids; D010455:Peptides; D011506:Proteins; C508725:Trp-cage peptide