title: Simulated Q-annealing: conformational search with an effective potential.
abstract: We have tested a version of the generalized simulated annealing algorithm based on molecular dynamics simulations with effective potential suggested by Tsallis statistics. The generalized annealing method, termed "simulated Q-annealing (SQ)," is applied to the simulations of a synthetic 11-residue peptide segment (1AQG). In SQ, the energy barriers between local minima change as the parameter q is varied and specific degrees of freedom can be selectively heated up and annealed. Conformational dynamics obtained by ordinary simulated annealing (SA) and SQ simulations are compared in order to illustrate the effectiveness of the SQ approach in conformational searching. We show that SQ can navigate the potential energy surface efficiently with a simple annealing protocol and demonstrate that conformations sampled by SQ can represent the funnel-like free energy surface.
authors.affiliation: School of Chemistry, Seoul National University, Seoul, Korea.
authors.forename: Won-joon
authors.initials: WJ
authors.lastname: Son
authors.forename: Soonmin
authors.initials: S
authors.lastname: Jang
authors.forename: Seokmin
authors.initials: S
authors.lastname: Shin
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins