Tues June 5 3pm Grp meeting
*************
   Victoria: explain dA:dT, TpA, etc... notations for DNA sequences
   REVIEW:  /autotmb/home/tmbshare/refs/Luge1997.pdf


Wed-Fri June 6-8
*****************
Continue to run some namd simulations, make some graphs of the output
and update a python script that James Solow and I started on.

Take a look at  the files in
/autotmb/home/bishop/Public/REU-RET2012/bin
specifically : namdenr, namdplot
the two py files will be ones that you edit

copy all of these to your bin directory i.e. to ~/bin/ or equivalently /home/USERNAME/bin/

to run the simulations in the back ground I've updated the files in
/autotmb/home/bishop/Public/REU-RET2012/NAMD/hormone-receptor

you should be able to make the same updates to the Nucleosome directory

copy run-namd-backgrnd.tcsh and 1ere-e2-backgrnd.conf
to whatever directory you have been working in.

in a shell you can start namd in the background with
the command
./run-namd-backgrnd.tcsh 20 > some.log &

this will run namd on 20 processors (you should use 4 or less) and output to "some.log"

once done
namdplot BOND ANGLE DIHED IMPR ELECT VDW vs TS some.log
will make a pretty plot of the output
you can also start up VMD to see what happened and read the log file in VMD


Thursday June 7
*****************
3PM group meeting
	running namd for the nucleosome and hormone-receptor examples
	using python
	see python documentation at 	
	http://www.python.org/doc/

Friday June 8
***************
GOAL: reprocess the namd outputs (dcd files) to generate energies for a subset of the atoms in the system
	using the gui in vmd or via command line  tools

Rocky and James working on FFT's in python
Toria: ? should be running namd/vmd to extract energies from saved dcd files for nucleosome

Week of June 11-15
**********************
Begin working with Bishop's data files
	-convert dcd to helical parm files for rajib's nucleosome sims
	-extract protein-DNA  interaction and DNA self energy from rajib's nucleosome sims



Week of June 26
*****************
-development of python scripts for helical paramter analysis
	-convert standard tasks to subroutines or modules that we'll use
	
-get nucleosome sims running for any sequence 
	-include helix parmeter extraction
	-include protein-dna interaction energies