9:45 am – 12:15 am
Project 2
- see post
Chromatin
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
- see post