title: Replica-exchange-with-tunneling for fast exploration of protein landscapes.
abstract: While the use of replica-exchange molecular dynamics in protein simulations has become ubiquitous, its utility is limited in many practical applications. We propose to overcome some shortcomings that hold back its use in settings such as multi-scale or explicit solvent simulations by integrating ideas of hybrid MC/MD into the replica-exchange protocol. This Replica-Exchange-with-Tunneling method is tested by simulating the Trp-cage protein, a system often used in molecular biophysics for testing sampling techniques.
authors.affiliation: Department of Physics Engineering, Hacettepe University, Beytepe-Ankara 06800, Turkey.
authors.forename: Fatih
authors.initials: F
authors.lastname: Yaşar
authors.affiliation: Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Bernhardt
authors.affiliation: Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.
authors.forename: Ulrich H E
authors.initials: UH
authors.lastname: Hansmann
mesh_terms: D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins