From c84c708dd9b341a085d4841ef33fd76fcf221f1a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Sun, 2 Dec 2018 10:16:11 -0600
Subject: [PATCH] Updated persistence length to be a little bit shorter
---
mrdna/segmentmodel.py | 22 ++++++++++++++++++++--
mrdna/version.py | 2 +-
2 files changed, 21 insertions(+), 3 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 40ab067..be162ec 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2072,6 +2072,22 @@ class SegmentModel(ArbdModel):
# print("Helix {}: bps {}, beads {}, separation {}".format(s.name, s.num_nt, beadsum, sepsum))
""" Add intrahelical angle potentials """
+ def get_effective_dsDNA_Lp(sep):
+
+ """ The persistence length of our model was found to be a
+ little off (probably due to NB interactions). This
+ attempts to compensate """
+
+ ## For 1 bp, Lp=559, for 25 Lp = 524
+ beads_per_bp = sep/2
+ Lp0 = 147
+ # return 0.93457944*Lp0 ;# factor1
+ return 0.97*Lp0 ;# factor2
+ # factor = bead_per_bp * (0.954-0.8944
+ # return Lp0 * bead_per_bp
+
+ empirical_compensation_factor = max_basepairs_per_bead
+
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
@@ -2080,7 +2096,8 @@ class SegmentModel(ArbdModel):
kT = 0.58622522 # kcal/mol
if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D":
- k = angle_spring_from_lp(sep,147)
+ Lp = get_effective_dsDNA_Lp(sep)
+ k = angle_spring_from_lp(sep,Lp)
if local_twist:
k_dihed = 0.25*k
k *= 0.75 # reduce because orientation beads impose similar springs
@@ -2134,7 +2151,8 @@ class SegmentModel(ArbdModel):
parent = self._getParent( b1, b2 )
""" Add heuristic 90 degree potential to keep orientation bead orthogonal """
- k = 0.5*angle_spring_from_lp(sep,147)
+ Lp = get_effective_dsDNA_Lp(sep)
+ k = 0.5*angle_spring_from_lp(sep,Lp)
pot = self.get_angle_potential(k,90)
parent.add_angle(o1,b1,b2, pot)
parent.add_angle(b1,b2,o2, pot)
diff --git a/mrdna/version.py b/mrdna/version.py
index 80ef677..b12c139 100644
--- a/mrdna/version.py
+++ b/mrdna/version.py
@@ -133,7 +133,7 @@ def get_version(abbrev=7):
if __name__ == "__main__":
- print( get_git_version() )
+ print( get_version() )
def read_version_file(filename):
with open(filename) as fh:
--
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