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Donnini S, Tegeler F, Groenhof G, et al. Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput. 2011;7(6):1962-1978doi: 10.1021/ct200061r.
Donnini, S., Tegeler, F., Groenhof, G., & Grubmüller, H. (2011). Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. Journal of chemical theory and computation, 7(6), 1962-1978. https://doi.org/10.1021/ct200061r
Donnini, Serena, et al. "Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics." Journal of chemical theory and computation vol. 7,6 (2011): 1962-1978. doi: https://doi.org/10.1021/ct200061r
Donnini S, Tegeler F, Groenhof G, Grubmüller H. Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput. 2011 Jun 14;7(6):1962-1978. doi: 10.1021/ct200061r. Epub 2011 Apr 25. PMID: 21687785; PMCID: PMC3114466.
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J Chem Theory Comput. 2011 Jun 14;7(6):1962-1978. doi: 10.1021/ct200061r. Epub 2011 Apr 25.

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics.

Journal of chemical theory and computation

Serena Donnini, Florian Tegeler, Gerrit Groenhof, Helmut Grubmüller

Affiliations

  1. Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Göttingen, Germany.

PMID: 21687785 PMCID: PMC3114466 DOI: 10.1021/ct200061r

Abstract

pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent.

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