title: Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm.
abstract: We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves numerical stability of simulations. In addition, the MSREMD method can also simplify a replica-exchange routine by eliminating velocity scaling. As a pilot system, a Lennard-Jones fluid is simulated with the new method. The results suggest that the MSREMD method improves the numerical stability at high temperatures compared with the conventional REMD method. For the Nosé-Hoover thermostats, we analytically demonstrate that the MSREMD simulations can reproduce completely the same trajectories of the conventional REMD ones with shorter time steps at high temperatures. Accordingly, we can easily compare the computational costs of the REMD and MSREMD simulations. We conclude that the MSREMD method decreases the instability and optimizes the computational resources with simpler algorithm.
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Siga 525-8577, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Nagai
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Siga 525-8577, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Takahashi
mesh_terms: D000465:Algorithms; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation