title: Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.
abstract: Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.
authors: Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439-8643, USA.
authors: Brian K
authors: BK
authors: Radak
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637-1454, USA.
authors: Benoît
authors: B
authors: Roux