From ed819c4bee0013c065b4ee57f9eb19e05ae9fc92 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 13 Jul 2018 18:42:45 -0500
Subject: [PATCH] Added an intrahelical angle potential between orientation
beads
---
segmentmodel.py | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/segmentmodel.py b/segmentmodel.py
index 9018fc4..20ca571 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -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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