Group Meetings

Wed April 2013 8Am
*********************

coarse grain models nucleosome and chromatin
i

TODO:
	primo-primona: 
		install and use on our system
		is there a nucleosome sim w/ this 
		http://feig.bch.msu.edu/main-research-methodology.html


TOM has to install primo/primona
 and send info to other



Wed May 1 2013 8am
***********************
SOme items:
1) coarse grained modeling 
	Primo-primona won't yet work I contacted the M. Feig
	this is not yet releasable

2) find way to parameterize nucleosome with expresso
    I need a summary of parameters for DNA/histone see the papers by Korolev2012

3) espresso tutorial
see http://espressomd.org/
and look for local install in 
/usr/local/espresso-3.1.2/
to turn it type 
/usr/local/espresso-3.1.2/Espresso
note Espresso is tcl based so espresso scripts work like VMD scripts

on our machines (DNA,ade,etc...) see
/usr/local/espresso-3.1.2/doc/tutorials/

use putty ssh to access dna
to run espresso you simply type
/usr/local/espresso-3.1.2/Espresso
and this puts you in an "esprsso" shell


4) VMD timeline plug-in...  we'll use this to process the nucleosome simulatoin data
http://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/

5) we have windows on our machines... (maybe)

6) collect talks and presentations that folks have given.
6a) chem. advisory meeting Friday... need nuggets

7) plans for next few weeks/summer... news on LBRN.
	routing forms?

Bishop went brain dead again.... so w2e can get by w/ online.
unless you are on the way... keep coming if not take a look at this.

 
Wed May 8 2013
*********************

see 
http://dna.engr.latech.edu/~bishop/Lab/Notes/2013/May2013.txt


anyupdates on espresso tutorials from folks?

any updates on vmd timeline tutorial from folks?

Torie's proposal routing info is being proceessed.

Bishop has run 100's of sims on kraken... that datta is coming in.
so we'll run analysis similar to last summers.

A stack of new HDs is coming so I'll be playing w/ HW and OS and moving filed next week...hope to get windows up/installed on all machines by then.

Will also separate data server from home directory server....
the curretns sims cause some slowdowns in user home when data is syncing.


OTHER NEWS ?


Wed May 15 2013
*********************
work w/ Will on PLOS logo
working thru espresso
	plan for a chromatin model
		nucleosome + DNA 
		where DNA = 5bp bead 
		nucleosome = entire histone + DNA and same vdw interact as DNA-DNA
				nucleosome = 3pt particle:  C.o.M + entry/exit beads 
				these then connect to DNA   C3P



Wed May 22 2013
******************
Stehr 2008 & Kepper 2008
vs. Woodcock 1993

Stehr:
	3 Shape



Wed. May  28
******************
see about running lammps 
	2d example of ellpisoids & spheres in fluid
	then 2d w/ just ellipsoids
	then 3d w/ just ellipsoids