Tuesday 07/01/14

7:30 am – 12:25 am

Goals

  • finish probe making
  • compute scaling of sub-paths through condensed sticky globules
  • revise fig 2 for oligo secondaries
  • write caption for fig 2 for olgio secondaries
  • write new discussion section corresponding to fig 2 for oligo secondaries.

Oligo secondaries paper

  • working on figure 2
  • wrote draft caption for fig 2
  • working on revising main text.
  • working on supp fig 14
  • working on XZ’s revisions round 2

Probe making

  • label probes,
  • test stain new cells with D08-D12-p3

Meetings

  • send email to LM
  • meeting with Anton, discuss preventing polymer explosions — see notes
  • send Matlab Steve viewing code to Hao

Cell staining

  • new stains,
    1. C02-P1-405 + S1-A647,
    2. E05-P1-405 + S1-A647,
    3. D08toD12-P3-405 + S3-A647 1.5 uL each probe
    4. L2F03-05 P3-405 + S3-A647 + L2F06-P1-405 (40 uL) 1.5 uL each probe

Coding notes

  • running MirnyStickyTemplateV6 with (global) energyMinimization, variableLangevin integrator, and SmoothSquareWellTailedForce for specific attractions.

    a = SimulationWithBonds(timestep=20, thermostat=0.05)
    a.setup(platform=platform, verbose=True, GPU=GPU,integrator="variableLangevin",errorTol=.0001)

    SimulationWithBonds inherits from Simulation and I’ve just added my own potentials here rather than modify openmmlib.py.
    Does it matter what I put for timestep if I’m using “variableLangevin” integrator? Have I specified the error tolerance for the variable integrator correctly?
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