Saturday 06/21/14

9:30 am – 5:45 pm

Simulations

To Analyze

  • OpenMM free Polymer sims
  • Odyssey Matlab periodic bonds

OpenMM free Polymers

Only a single run, but not quite the right scaling — expect 0.60. And a y-intercept at 0. See previous simulations results using my monte carlo simulator in Matlab

FreePolymerOpenMMscaling

This is still growing substantially faster than closest packing.

Running new simulations with more repeats (4) and smaller polymers (only up to 500 — the large ones really take forever).

Matlab Periodically bound polymers

Not enough simulation time for binding nodes to find each other. Some succeed, some do not.

NotConnected

MostlyConnected

Future development

  • wrote to RC computing about installing OpenMM and openMM-polymer on Odyssey.

STORM

  • imaging D04
  • sample not too bright. Hopefully still enough localizations to map out the basic structure.
This entry was posted in Summaries. Bookmark the permalink.