Distinguished Lecture Series Guest Speaker:
Department of Chemistry
Systems with multiple free energy minima pose challenges to conventional methods of computer simulation due to broken ergodicity, which may be overcome or mitigated with generalized ensembles. STMD  is a MD algorithm sampling a flat-energy distribution, and GREM  is a replica exchange algorithm in which the replicas are explicitly designed to sample states with coexisting phases. The application and performance of STMD, the replica exchange version, RESTMD , and the GREM will be detailed for biomolecules and for phase equilibrium.
1. Jae Gil Kim, J. E. Straub and T. Keyes, Statistical Temperature Monte Carlo and Molecular Dynamics Algorithms, Phys. Rev. Lett. 97, 050601 (2006); Jae Gil Kim and T. Keyes, The Influence of Energetic Frustration on the Global Shapes of Energy Landscapes in beta-Barrel Forming Model Proteins: Inherent Structure Analysis and Statistical Temperature Molecular Dynamics Simulation, J. Phys. Chem. B 112, 954 (2008).
2. Jaegil Kim, Thomas Keyes and John E. Straub, Generalized Replica Exchange Method, J. Chem. Phys. 132, 224107 (2010).
3. Jaegil Kim, John E. Straub and Tom Keyes, Replica Exchange Statistical Temperature Molecular Dynamics Algorithm, J. Phys. Chem. B 116, 8646 (2012).