title: Replica exchange statistical temperature molecular dynamics algorithm.
abstract: The replica exchange statistical temperature molecular dynamics (RESTMD) algorithm is presented, designed to alleviate an extensive increase of the number of replicas required as system size increases in the conventional temperature replica exchange method (tREM), and to obtain improved sampling in individual replicas. RESTMD optimally integrates multiple STMD (Phys. Rev. Lett. 2006, 97, 050601) runs with replica exchanges, giving rise to a flat energy sampling in each replica with a self-adjusting weight determination. The expanded flat energy dynamic sampling range allows the use of significantly fewer STMD replicas while maintaining the desired acceptance probability for replica exchanges. The computational advantages of RESTMD over conventional REM and single-replica STMD are explicitly demonstrated with an application to a coarse-grained protein model. The effect of two different kinetic temperature control schemes on the sampling efficiency is explored for diverse simulation conditions.
authors.affiliation: Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States. jaegilkim89@gmail.com
authors.forename: Jaegil
authors.initials: J
authors.lastname: Kim
authors.forename: John E
authors.initials: JE
authors.lastname: Straub
authors.forename: Tom
authors.initials: T
authors.lastname: Keyes
mesh_terms: D000465:Algorithms; D007700:Kinetics; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins