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mrdna
Commits
ce97ef38
Commit
ce97ef38
authored
Oct 27, 2018
by
cmaffeo2
Browse files
Added dihedral angle to DNA backbone for model with twist to obtain correct persistence length
parent
e13731db
Changes
2
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Inline
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mrdna/segmentmodel.py
View file @
ce97ef38
...
...
@@ -2082,11 +2082,11 @@ class SegmentModel(ArbdModel):
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
)
if
local_twist
:
## TODO optimize this paramter
k
*=
0.5
#
halv
e because orientation beads
hav
e similar springs
angle
=
self
.
get_
angle
_potential
(
k
,
180
)
o
1
,
o
2
,
o3
=
[
b
.
orientation_bead
for
b
in
(
b1
,
b2
,
b3
)]
parent
.
add_angle
(
o1
,
o2
,
o3
,
angle
)
k_dihed
=
0.25
*
k
k
*=
0.
7
5
#
reduc
e because orientation beads
impos
e similar springs
dihed
=
self
.
get_
dihedral
_potential
(
k
_dihed
,
180
)
parent
.
add_dihedral
(
b
1
,
b
2
,
b
2
.
orientation_bead
,
b3
,
dihed
)
else
:
## TODO: get correct number from ssDNA model
...
...
@@ -2138,7 +2138,7 @@ class SegmentModel(ArbdModel):
pot
=
self
.
get_angle_potential
(
k
,
90
)
parent
.
add_angle
(
o1
,
b1
,
b2
,
pot
)
parent
.
add_angle
(
b1
,
b2
,
o2
,
pot
)
## TODO: improve this
twist_per_nt
=
0.5
*
(
p1
.
twist_per_nt
+
p2
.
twist_per_nt
)
angle
=
sep
*
twist_per_nt
...
...
mrdna/simulate.py
View file @
ce97ef38
...
...
@@ -7,6 +7,8 @@ from . import get_resource_path
arbd
=
"/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd"
# reduced the mem footprint cause vmd
namd
=
"/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
## TODO: implement replicas, initial conditions specified through some restart, and a custom simulation schedule
def
multiresolution_simulation
(
model
,
output_name
,
job_id
=
None
,
gpu
=
0
,
...
...
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