Hamiltonian replica exchange

Fukunishi, O. Watanabe Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems application to protein structure prediction, J. Chem. Phys. 2002,116, 9058-9067... 

Affentranger, R., Tavernelli, I., Di lorio, E. E. (2006). A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling. Journal of Chemical Theory and Computation, 2, 217. 

Curuksu, J., Zacharias, M. (2009). Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach. Journal of Chemical Physics, 130,104110. 

Zacharias, M. (2008). Combining elastic network analysis and molecular dynamics simulations by Hamiltonian replica exchange. Journal of Chemical Theory and Computation, 4, 477. 

Widmalm et al. have studied conformational sampling for a set of ten a- or p-(l - 6)-linked oligosaccharides using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. In this work the authors have evaluated 7(H,H), using... 

Widmalm and coworkers combine NMR transglycosidic J coupling constants and explicit solvent Hamiltonian replica exchange simulations to improve and validate the CHARMM36 force field as well as their simulation method on a set of a- or p-(l- 6)-linked oligosaccharides. The experimental trends in rotamer distributions are reproduced in simulations. Walker and coworkers report a new AMBER14 FF for lipids which is validated against NMR data. The philosophy is to be compatible with AMBER FFs for proteins and nucleic acids. ... 

H. Fukunishi, O. Watanabe, and S. Takada,/. Chem. Phys., 116(20), 9058-9067 (2002). On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems Application to Protein Structure Prediction. 

W. Jiang and B. Roux,/. Chem. Theory Comput., 6(9), 2559-2565 (2010). Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. 

This chapter highlighted the use of replica exchange molecular dynamics calculations for the investigation of the performance of the PM3, PDDG/PM3 and PM3PC Hamiltonians as applied for the conformational equilibrium of alanine dipeptide in the gas phase and water solution, a convenient model system for the study of biological molecules. 

Additionally, non-Hamiltonian d5mamics can be used in applications/ methodologies such as Path-integral MD, replica-exchange methods, variable transformation techniques, free energy dynamics methods, and other new applications. Generating these alternative statistical ensembles from simulation requires the use of extended systems or extended phase space [9]. In these systems, the simulations do not only include the N coordinate and momentum vectors that are needed to describe a classical Ai-particle system, but they also include a set of additional control or extended variables that are used to drive the fluctuations required by the ensemble of interest. 

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