Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

@article{Machuqueiro2006ConstantpHMD,
  title={Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.},
  author={Miguel Machuqueiro and Ant{\'o}nio M Baptista},
  journal={The journal of physical chemistry. B},
  year={2006},
  volume={110 6},
  pages={
          2927-33
        }
}
A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil… CONTINUE READING

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