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slab.TODO.txt
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slab.TODO.txt
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TODO:
AnchorToToroidalPorePairScore:
- TBD
Statistics:
- TBD
BrownianDynamicsTAMDWithSlabSupport.h/cpp
- add slab parameter, that will be optimized (radius variable should be given fake diffusivity constant, and then be subjected to brownian motion, including applied forces)
automatic_parameters.cpp
- include tunnel_radius_k and anchor_k in step size calculations? (or assume it's slow relative to other motions?)
TESTS -
- SlabWithToroidalPorePairScore
- AnchorToCylindricalPorePairScore
- All other new features that were recently implemented (see below)
RMF support:
- TBD (need to take care of dynamic pore size mainly - quite a pain to display)
Output file:
- TBD (except statistics, updating latest radius?)
Future options:
- for efficiency - make a single restraint for Anchor to Cylindrical Pore Pair Score (by adding PoreAnchor decorator that includes normalized xy and pore radial d, also link this to RMF
DONE:
=====
Scoring:
- add add_restrained_anchor_bead() method, with AnchorToCylinderriclPairScore (or Toroidal TBD) on anchor points, if tunnel_radius_k>0, with shift defined based on initial shift (what happens upon restart?)
- add slab restraint based on PoreRadiusSingleionScore if get_sd()->tunnel_radius_k>0
- include pore radius restraint and anchor restraints in scoring function (probably both custom and non-custom)
npctransport.proto
- k for slab radius; if <=0 -> static slab radius (non-optimized)
Simulation data
- read tunnel_radius_k
- define CylindricalPoreAnchorPairScore (or Toroidal TBD) on anchor points, if tunnel_radius_k>0, with shift defined based on initial shift (what happens upon restart?)
- call scoring to add restraints on anchors to pore if tunnel_radius_k>0 and anchor_k>0
PoreRadiusSinglestonScore
- a score on the pore radius equilibrium value, parameters: equilibrium radius, k
AnchorToCylidnricalPorePairScore
- evaluate_index(slab, particle) is a distance restraint on particle, relative to a location in spherical coordinates - fixed angle and z, at current pore radius. (harmonic) - pore radius derivative affected by projection of pulling force over radial axis; allow adding a shift relative to radius (+ = inside; - = outside, r=0 as minimum)
TESTS
- updated SlabWithCylindricalPorePairScore
- PoreRadiusSingletonScore