Commit ed819c4b authored by cmaffeo2's avatar cmaffeo2
Browse files

Added an intrahelical angle potential between orientation beads

parent 5d9a95a9
......@@ -1709,6 +1709,10 @@ class SegmentModel(ArbdModel):
if local_twist:
## TODO optimize this paramter
k *= 0.5 # halve because orientation beads have similar springs
angle = self.get_angle_potential(k,180)
o1,o2,o3 = [b.orientation_bead for b in (b1,b2,b3)]
parent.add_angle( o1, o2, o3, angle )
else:
## TODO: get correct number from ssDNA model
k = 1.5 * kT * (1.0 / (1-np.exp(-float(sep)/3))) * 0.00030461742; # kcal_mol/degree^2
......
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