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,
- C02-P1-405 + S1-A647,
- E05-P1-405 + S1-A647,
- D08toD12-P3-405 + S3-A647 1.5 uL each probe
- 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?