Replica-exchange conformational sampling

We applied replica exchange molecular dynamics (REMD) calculations for conformational sampling of the AD in explicit water, where the AD is treated quantum mechanically and the water molecules classically, using the TIP3P [29] model. For comparison purposes, the same calculation is done where the AD is treated by a classical force field, using our recently developed AMBER ff99SB [30] parameters. 

Kannan, S., 8c Zacharias, M. (2009). Simulated annealing coupled replica exchange molecular dynamics - an efficient conformational sampling method. Journal of Structural Biology, 166, 288. 

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. 

Kannan, S., Zacharias, M. (2007b). Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins, 66, 697. 

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... 

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