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tbgl
tools
mrdna
Commits
ed819c4b
Commit
ed819c4b
authored
Jul 13, 2018
by
cmaffeo2
Browse files
Added an intrahelical angle potential between orientation beads
parent
5d9a95a9
Changes
1
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Inline
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segmentmodel.py
View file @
ed819c4b
...
...
@@ -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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