Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

J Chem Theory Comput. 2017 Nov 14;13(11):5647-5657. doi: 10.1021/acs.jctc.7b00508. Epub 2017 Oct 27.


The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.

MeSH terms

  • Ciclopirox
  • Copper Transport Proteins
  • Humans
  • Hydrogen Bonding
  • Metallochaperones / chemistry
  • Models, Molecular
  • Molecular Chaperones
  • Molecular Dynamics Simulation*
  • Proteins / chemistry*
  • Pyridones* / chemistry
  • Solvents
  • Strychnine / chemistry
  • Thermodynamics
  • Water / chemistry*


  • ATOX1 protein, human
  • Copper Transport Proteins
  • Metallochaperones
  • Molecular Chaperones
  • Proteins
  • Pyridones
  • Solvents
  • Water
  • Ciclopirox
  • Strychnine