Commit c1d8f2fe authored by cmaffeo2's avatar cmaffeo2
Browse files

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
parent 91b7e700
......@@ -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',
......
......@@ -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',
......
......@@ -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)
......
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