title: Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement.
abstract: Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data. We here propose a scheme based on the maximum entropy principle to combine simulations with bulk experiments. In the proposed scheme, the noise arising from both the measurements and the forward models used to back-calculate the experimental observables is explicitly taken into account. The method is tested on RNA nucleosides and is then used to construct chemically consistent corrections to the Amber RNA force field that allow a large set of experimental data on nucleosides and dinucleosides to be correctly reproduced. The transferability of these corrections is assessed against independent data on tetranucleotides and displays a previously unreported agreement with experiments. This procedure can be applied to enforce multiple experimental data on multiple systems in a self-consistent framework, thus suggesting a new paradigm for force field refinement.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati (SISSA) , via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cesari
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati (SISSA) , via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Gil-Ley
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati (SISSA) , via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussi
mesh_terms: D000465:Algorithms; D019277:Entropy; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA