title: Applying efficient implicit nongeometric constraints in alchemical free energy simulations.
abstract: Several strategies have been developed for satisfying bond lengths, angle, and other geometric constraints in molecular dynamics simulations. Advanced variations of alchemical free energy perturbation simulations, however, also require nongeometric constraints. In our recently developed multisite λ-dynamics simulation method, the conventional λ parameters that are associated with the progress variables in alchemical transformations are treated as dynamic variables and are constrained such that: 0 ≤ λ(i) ≤ 1 and Σ(i = 1)(N) λ(i) = 1. Here, we present four functional forms of λ that implicitly satisfy these nongeometric constraints, whose values and forces are facile to compute and that yield stable simulations using a 2 fs integration timestep. Using model systems, we present the sampling characteristics of these functional forms and demonstrate the enhanced sampling profiles and improved convergence rates that are achieved by the functional form: λ(i) = e(c sinθ(i))/Σ(j = 1)(N) e(c sinθ(j)) that oscillates between λ(i) = 0 and λ(i) = 1 and has relatively steep transitions between these endpoints.
authors.affiliation: Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Knight
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics