Made beads have half-harmonic repulsion at distances < 13 AA to prevent strand crossings

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):