Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems.
A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF method have fixed internal structures and frozen electron densities. The hybrid method provides a seamless description of the boundary between the subsystems and allows for the flow of molecules across the boundary. Tests on a liquid water system show that the total energy is conserved well during molecular dynamics and that the effect of the solvent environment on the KS subsystem is well described. An initial application to copper ion binding to the prion protein is also presented.
Hodak
Miroslav
M
Center for High Performance Simulation and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-7518, USA. hodak@chips.ncsu.edu
Lu
Wenchang
W
Bernholc
J
J
D003198:Computer Simulation; D003300:Copper / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry; D011328:Prions / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D011328:Prions; D014867:Water; D003300:Copper; D006859:Hydrogen