From 9620a049492b21ad433748d54be2d66d6ba8a254 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 30 Apr 2019 17:22:06 -0500
Subject: [PATCH] Made beads have half-harmonic repulsion at distances < 13 AA
to prevent strand crossings
---
mrdna/model/nbPot.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/mrdna/model/nbPot.py b/mrdna/model/nbPot.py
index 1ad9022..305d34b 100644
--- a/mrdna/model/nbPot.py
+++ b/mrdna/model/nbPot.py
@@ -72,6 +72,7 @@ class AbstractNbDnaScheme(NonbondedScheme):
u = interp1d(x0, np.array(parms),
bounds_error = False, fill_value="extrapolate",
assume_sorted=True)(x).T
+ u[x<13] = u[x<13] + 0.5 * (x[x<13]-13)**2
return u-u[-1]
def get_bead_distributions(self, interhelical_distances):
--
GitLab