From c7ef30bfe7156e34f5805f33dbe60d43343c029c Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 17 Oct 2018 12:02:05 -0500
Subject: [PATCH] Fixed double-counting of contour length for angle potential
---
mrdna/segmentmodel.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 80436df..13a5d74 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2075,7 +2075,7 @@ class SegmentModel(ArbdModel):
if self.DEBUG: print("Adding intrahelical angle potentials")
for b1,b2,b3 in self._get_intrahelical_angle_beads():
## TODO: could be slightly smarter about sep
- sep = 0.5*b1.num_nt+b2.num_nt+0.5*b3.num_nt
+ sep = 0.5*(0.5*b1.num_nt+b2.num_nt+0.5*b3.num_nt)
parent = self._getParent(b1,b2,b3)
kT = 0.58622522 # kcal/mol
--
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