diff --git a/bin/enrgmd b/bin/enrgmd index cd8627d5650a95ce0894f2b3709405d8bae0d276..4a8cf0e977ca709898f2968314d6e78bf243f349 100755 --- a/bin/enrgmd +++ b/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', diff --git a/bin/mrdna b/bin/mrdna index 01686bb47e17c12dab2d3e3fa133b9cce1edf0ed..1645aa553007fd9951dce45fd2177ae2311cd0cf 100755 --- a/bin/mrdna +++ b/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', diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py index ff4f2d6f08066d013fcd1d0326e0d98ea026b67b..3071839fed87cbef72860e8c738d0f698b294379 100644 --- a/mrdna/segmentmodel.py +++ b/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)