title: Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.
abstract: Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, 2000 East 30 South Skaggs 201, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: Niel M
authors.initials: NM
authors.lastname: Henriksen
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Roe
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D000409:Alanine / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009841:Oligonucleotides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
chemical_list: D004151:Dipeptides; D009841:Oligonucleotides; D012997:Solvents; D000409:Alanine