title: Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.
abstract: Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 2000 South 30 East Room 105, Salt Lake City, Utah 84112, United States.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Roe
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D016000:Cluster Analysis; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012313:RNA