Friday 10/10/14

9:45 am – 12:15 am

Project 2

  • see post


Openmm configuration

  • updated openmm-polymer in Python26/Lib/site-packages/ to latest download
  • archived old openmm-polymer in Research/Software/OpenMMchromatin/Archive (this had some of my scripts as well)
  • reorganizing OpenMMchromatin into
    • Archive
    • Templates
    • Simulations
    • Functions
    • Scratch

Coding with Bogdan

  • Realization: should only look at scaling much shorter than constrained volume traversal.
    • the flat scaling in fractal globules is just after the polymer reaches the boundaries of confinement
    • sticky polymers set their own boundaries based on the size of the ball in which the nodes of the polymer still have sufficient contact.
  • implemented variable stiffness simulation
  • implemented variable stickiness simulation

Chromatin simulation results

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