diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py index 13a5d74462259059836791a4621a9f1402c074d5..40ab067a42792d1fa8fb0dcb6182b2284346c55d 100644 --- a/mrdna/segmentmodel.py +++ b/mrdna/segmentmodel.py @@ -2082,11 +2082,11 @@ class SegmentModel(ArbdModel): if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D": k = angle_spring_from_lp(sep,147) if local_twist: - ## TODO optimize this paramter - k *= 0.5 # halve because orientation beads have similar springs - angle = self.get_angle_potential(k,180) - o1,o2,o3 = [b.orientation_bead for b in (b1,b2,b3)] - parent.add_angle( o1, o2, o3, angle ) + k_dihed = 0.25*k + k *= 0.75 # reduce because orientation beads impose similar springs + dihed = self.get_dihedral_potential(k_dihed,180) + parent.add_dihedral(b1,b2,b2.orientation_bead,b3, dihed) + else: ## TODO: get correct number from ssDNA model @@ -2138,7 +2138,7 @@ class SegmentModel(ArbdModel): pot = self.get_angle_potential(k,90) parent.add_angle(o1,b1,b2, pot) parent.add_angle(b1,b2,o2, pot) - + ## TODO: improve this twist_per_nt = 0.5 * (p1.twist_per_nt + p2.twist_per_nt) angle = sep*twist_per_nt diff --git a/mrdna/simulate.py b/mrdna/simulate.py index 7494f9b0ed51a28ea77223befe075845006b12b5..2e0464791a84a7e013feb5037eb9af63d3502e92 100644 --- a/mrdna/simulate.py +++ b/mrdna/simulate.py @@ -7,6 +7,8 @@ from . import get_resource_path arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2" +## TODO: implement replicas, initial conditions specified through some restart, and a custom simulation schedule + def multiresolution_simulation( model, output_name, job_id=None, gpu = 0,