title: Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent.
abstract: We propose a scheme for replica exchange molecular dynamics of proteins in explicit solvent that minimizes the number of required replicas using velocity rescaling. Our approach relies on a hybrid method where the protein evolves at each temperature in an explicit solvent, but replica exchange moves utilize an implicit solvent term. The two terms are coupled through the velocity rescaling. We test the efficiency of this approach for a common test case, the trp-cage protein.
authors: Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. wangjinanzhl@sina.com
authors: Jinan
authors: J
authors: Wang
authors: Weiliang
authors: W
authors: Zhu
authors: Guohui
authors: G
authors: Li
authors: Ulrich H E
authors: UH
authors: Hansmann
mesh_terms: D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*
chemical_list: D011506:Proteins; D012997:Solvents