From 7732a822b405be1a65d591ababd2928128e3505a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 13 Aug 2019 15:15:52 -0500
Subject: [PATCH] Made oxDNA configuration writer use arbdmodel.debye_length if
salt_concentration not provided
---
mrdna/model/arbdmodel.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index b374901..d2d791b 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -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 = ''
--
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