title: Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.
abstract: A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.
authors.affiliation: Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan. ymori@ims.ac.jp
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Mori
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamoto
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011522:Protons
chemical_list: D011522:Protons