Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects

@article{FaraldoGmez2007CharacterizationOC,
  title={Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects},
  author={Jos{\'e} D. Faraldo-G{\'o}mez and Beno{\^i}t Roux},
  journal={Journal of computational chemistry},
  year={2007},
  volume={28 10},
  pages={1634-47}
}
Molecular dynamics simulations based on the replica-exchange framework (REMD) are emerging as a useful tool to characterize the conformational variability that is intrinsic to most chemical and biological systems. In this work, it is shown that a simple extension of the replica-exchange method, known as Hamiltonian REMD, greatly facilitates the characterization of conformational equilibria across large energetic barriers, or in the presence of substantial entropic effects, overcoming some of… CONTINUE READING
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