First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes - Multiscale Molecular Methods in Applied Chemistry - page 29

Fig. 14 Meso-scale model of
DNA

where E Bonds , E Angles , and E Torsions take the same form as those in Fig. 3 , while the
E nonBond corresponds to a Morse type potential:

h i

;

ð Þ ð Þ

D 0 e a 1 þr i j r 0

=

2e 0 : 5 a 1 þr ij r 0

=

E nonBond ¼ (17)

and the E hBond :

cos 4

12 6

r 0
r

r 0
r

E hBond ¼ D 0 5 6 y; (18)

where corresponds to the angle between a hydrogen and the corresponding

donor-acceptor pair.

y

Coarse-Grain Parameter Optimization

The snapshots used when computing the nearest neighbor parameters are analyzed
over 1,049 structures. For each snapshot, atoms comprising each pseudo-atom were
determined. The center of mass of these atoms was then computed and the
corresponding pseudo-atoms were placed at this center of mass.

Valence Parameters

Each snapshot was iteratively traversed and the two body bond lengths, three body
angles, and four body dihedrals calculated from the positions of the pseudo-atoms.