Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tbgl
tools
mrdna
Commits
7732a822
Commit
7732a822
authored
Aug 13, 2019
by
cmaffeo2
Browse files
Made oxDNA configuration writer use arbdmodel.debye_length if salt_concentration not provided
parent
5455d407
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/model/arbdmodel.py
View file @
7732a822
...
...
@@ -1255,7 +1255,7 @@ E = 0 0 0
log_file
,
num_steps
=
1e6
,
interaction_type
=
'DNA2'
,
salt_concentration
=
0.5
,
salt_concentration
=
None
,
print_conf_interval
=
None
,
print_energy_every
=
None
,
timestep
=
0.003
,
...
...
@@ -1294,7 +1294,14 @@ E = 0 0 0
if
max_backbone_force
is
not
None
:
max_backbone_force
=
'max_backbone_force = {}'
.
format
(
max_backbone_force
)
if
interaction_type
in
(
'DNA2'
,):
if
salt_concentration
is
None
:
try
:
## units "80 epsilon0 295 k K / (2 (AA)**2 e**2/particle)" mM
salt_concentration
=
9331.3126
/
self
.
debye_length
**
2
except
:
salt_concentration
=
0.5
salt_concentration
=
'salt_concentration = {}'
.
format
(
salt_concentration
)
else
:
salt_concentration
=
''
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment