ELECTRONIC-STRUCTURE-BASED MOLECULAR-DYNAMICS METHOD FOR LARGE BIOLOGICAL-SYSTEMS - APPLICATION TO THE 10-BASEPAIR POLY(DG)-CENTER-DOT-POLY(DC) DNA DOUBLE HELIX
Jp. Lewis et al., ELECTRONIC-STRUCTURE-BASED MOLECULAR-DYNAMICS METHOD FOR LARGE BIOLOGICAL-SYSTEMS - APPLICATION TO THE 10-BASEPAIR POLY(DG)-CENTER-DOT-POLY(DC) DNA DOUBLE HELIX, Physical review. B, Condensed matter, 55(11), 1997, pp. 6880-6887
Combining several recently developed theoretical techniques, we have d
eveloped an electronic-structure-based method for performing molecular
-dynamical simulations of large biological systems. The essence of the
method can be summarized in three points: (i) There are two energy sc
ales in the Hamiltonian and each is treated differently-the strong int
ramolecular interactions are treated within approximate density-functi
onal theory, whereas the weak intermolecular interactions (e.g., hydro
gen bonds) are described within a simple theory that accounts for Coul
omb, exchange, and hopping interactions between the weakly interacting
fragments. (ii) A localized basis of atomic states is used, yielding
sparse Hamiltonian and overlap matrices. (iii) The total energies and
forces from the sparse Hamiltonian and overlap matrices are solved usi
ng a linear scaling technique to avoid the N-3 scaling problem of stan
dard electronic structure methods. As an initial benchmark and test ca
se of the method, we performed calculations of a deoxyribonucleic acid
(DNA) double-helix poly(dG). poly(dC) segment containing ten basepair
s, with a total of 644 atoms. By a dynamical simulation, we obtained t
he minimum-energy geometry and the electronic structure of this DNA de
hydrated segment, as well as the full dynamical matrix corresponding t
o the relaxed structure. The vibrational data and energy band gap obta
ined compare qualitatively well with previous experimental data and ot
her theoretical results.