title: Improved Force Field Parameters Lead to a Better Description of RNA Structure.
abstract: We compare the performance of two different RNA force fields in four water models in simulating the conformational ensembles r(GACC) and r(CCCC). With the increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data to evaluate force field reliability. The combination of AMBER ff12 with vdW(bb) modifications and the OPC water model produces results in quantitative agreement with the NMR ensemble that have eluded us to date.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D012313:RNA