Use average persistence length of parent segments in model.simulate(), rather...

Use average persistence length of parent segments in model.simulate(), rather than object returned _get_parent(), which can be 'model'; thanks to Elija Feigl

bin/enrgmd

@@ -27,7 +27,7 @@ parser.add_argument('--crossover-to-intrahelical-cutoff', type=float, default=-1
 parser.add_argument('--backbone-scale', type=float, default=1.0,
                     help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
 
-parser.add_argument('--enrg-md-steps', type=int, default=1e6,
+parser.add_argument('--enrg-md-steps', type=float, default=1e6,
                     help='Number of ENRG-MD steps')
 
 parser.add_argument('--write-pqr', action='store_true',

bin/mrdna

@@ -70,7 +70,7 @@ parser.add_argument('--backbone-scale', type=float, default=1.0,
 parser.add_argument('--run-enrg-md', action='store_true',
                     help='Perform the ENRG-MD simulation?')
 
-parser.add_argument('--enrg-md-steps', type=int, default=1e6,
+parser.add_argument('--enrg-md-steps', type=float, default=1e6,
                     help='Number of ENRG-MD steps')
 
 parser.add_argument('--debug', action='store_true',

mrdna/segmentmodel.py

@@ -2932,9 +2932,10 @@ class SegmentModel(ArbdModel):
                     o1,o2 = [b.orientation_bead for b in (b1,b2)]
 
                     parent = self._getParent( b1, b2 )
-
+                    _Lp = (p1.persistence_length + p2.persistence_length) * 0.5
+                    
                     """ Add heuristic 90 degree potential to keep orientation bead orthogonal """
-                    k = 0.25*k_dsdna_angle(sep, parent.persistence_length)
+                    k = 0.25*k_dsdna_angle(sep, _Lp)
                     pot = self.get_angle_potential(k,90)
                     parent.add_angle(o1,b1,b2, pot)
                     parent.add_angle(b1,b2,o2, pot)