title: Application of the accelerated molecular dynamics simulations to the folding of a small protein.
abstract: In this paper, we further explore the applicability of the accelerated molecular dynamics simulation method using a bias potential. The method is applied to both simple model systems and real multidimensional systems. The method is also compared to replica exchange simulations in folding a small protein, Trp cage, using an all atom potential for the protein and an implicit model for the solvent. We show that the bias potential method allows quick searches of folding pathways. We also show that the choice of the bias potential has significant influence on the efficiency of the bias potential method.
authors.affiliation: Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Lijiang
authors.initials: L
authors.lastname: Yang
authors.forename: Michael Patrick
authors.initials: MP
authors.lastname: Grubb
authors.forename: Yi Qin
authors.initials: YQ
authors.lastname: Gao
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding
chemical_list: D010455:Peptides; C508725:Trp-cage peptide