Table 1. Parameters used in the coarse-grained model of double helical DNA.

Bonds/angle	Equilibrium distance/angle	Force constant	Comments
D-P*	9.62 Å	25 kT/Å2	Phosphate- central bead bond
D-D	6.8 Å	25 kT/Å2	Bond between neighbouring central beads
P1–P2; P3–P4; P2–P′1; P4-P′3	6.75 Å	25 kT/Å2	Bonds connecting neighbouring phosphates along each strand
P1–P′3; P2– P′4	13.2 Å	5 kT/Å2	Bonds across minor grove
D-D-D	180°	50 kT/rad2	Keeps DNA backbone
P1-P2-P′1; P2-P′1-P′2; P3-P4-P′3; P4-P′3-P′4	149°	100 kT/rad2	Angle along phosphate strands
P1-D-P3; P2-D-P4	140°	100 kT/rad2	Keeps angle between the two phosphate strands

Particles are marked as in Fig. 3A: phosphates P1 and P2 belong to one DNA strand; P3 and P4 belong to the other strand; P′1–P′4 are phosphates from the next unit (see Fig. 3).