From 0befffbe0dbb46d34a1e1eb522bbfeae492cccac Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 28 Jul 2020 10:20:32 -0500
Subject: [PATCH] Fixed oxDNA topology for circular strands; increased default
max_backbone_force
---
mrdna/segmentmodel.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 3234f10..b7603b7 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -3626,7 +3626,7 @@ E = 0 0 0
idx = 0
sidx = 1
for strand in strands:
- prev = idx+len(strand.num_nt) if strand.is_circular else -1
+ prev = idx+strand.num_nt-1 if strand.is_circular else -1
last = idx if strand.is_circular else -1
## Traverse 3'-to-5'
@@ -3666,7 +3666,7 @@ E = 0 0 0
delta_translation = 0.22,
delta_rotation = 0.22,
verlet_skin = 0.5,
- max_backbone_force = 5,
+ max_backbone_force = 100,
):
if seed is None:
--
GitLab