Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain.

@article{Kleinerman2008ImplementationsON,
  title={Implementations of Nos{\'e}-Hoover and Nos{\'e}-Poincar{\'e} thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain.},
  author={Dana S Kleinerman and Cezary Czaplewski and Adam Liwo and Harold A. Scheraga},
  journal={The Journal of chemical physics},
  year={2008},
  volume={128 24},
  pages={245103}
}
Molecular dynamics (MD) simulations generate a canonical ensemble only when integration of the equations of motion is coupled to a thermostat. Three extended phase space thermostats, one version of Nose-Hoover and two versions of Nose-Poincare, are compared with each other and with the Berendsen thermostat and Langevin stochastic dynamics. Implementation of extended phase space thermostats was first tested on a model Lennard-Jones fluid system; subsequently, they were implemented with our… CONTINUE READING