title: Nudged-elastic band used to find reaction coordinates based on the free energy.
abstract: Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration. The transition state can be refined by a Newton-Raphson search starting from the highest point of the NEB path. All optimizations are done using Cartesian coordinates. Independent molecular dynamics (MD) runs are performed at each image used to discretize the path. This makes the method intrinsically parallel. In contrast to other free energy methods, the algorithm does not become more expensive when including more degrees of freedom in the active space. The method is applied to the alanine-dipeptide as a test case and compared to pathways that have been derived from metadynamics and forward flux sampling.
authors.affiliation: Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
authors.forename: Matthias U
authors.initials: MU
authors.lastname: Bohner
authors.affiliation: Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Zeman
authors.affiliation: Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Smiatek
authors.affiliation: Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Arnold
authors.affiliation: Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Kästner
mesh_terms: D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; C002956:alanylalanine