June 2019 Group Labbook
****************

5/31/2019
*********

calendars and plans:
Ran
Zilong
Deonte	

CIMM:
	poster printed
	ICME talk

Albany:

Capruso:

SGCI:


6/5/2019
*******************
MISC:  ARFs/registration/reimbursements
	ARF for RSU and ZLI are good thru June 30
	will be extended thru summer and fall later in june
	zynthia/cimm is for Zilong
	brook/grad school is for Ran

	cimm-symp w/ rachel all done
	lbrn: alexis is checking
	
HW: disk space and reorganization of stuff
	relocate CIMMhub
	is cimmhub being backed up?
	networking
	
SW: Amber on DNA and on laptop
    notes from Deonte on linux
	config.
	cuda/opencl?
	integ w/ tmblab systems?
	root password?
CIMM: meeting take home?

Deonte:
	laptop config
		HD setup
		software config?
	nanocar: 
		refs/reviews
RSU: 
	albany poster
	review 601 figures and outline
	any new calcs to do?
ZLI: 
	loop model w/ 1CPN
	magic snake
	HPtools... where can we find it

Django; is there a "quick" tutorial/overview
	that does something




************************
Group meeting 6/19
***************

HW:

RNA:		
/dev/sda1        74T   68T  6.1T  92% /mount
	not actively used: full trajectories and OLD home data are here.

DNA:
/dev/sda1        66T   21T   45T  32% /raid6
	active/current home directory
	ibiomes all dewatered trajectories
		missing: dna:/raid6/projects/ trajectories
			and biologic sims pgpub and others from travers etc..
			dna:/autoOLD/simulations/biologic which is rna:/mount

ADE:
/dev/md127       20T   16T  3.4T  83% /raid5
		/scratch contains 2x 1uS 601 sims w/ water. the dewatered ones  are in ibiomes
		and old backups
			
SW:
	Amber18: installed on all + AmberTools19 ; installed on DNA
		must set environment variables
	deonte has it on the laptop. no he did not

Web: fix HTTPS for DNA
	lets encryp
	zilong upldate DNA this morning
		see email on 6/19  to bishoplab on how to do this
	this should be made into a cron job
	it's already done on cimmhub... have to older version


Science:
	ZLI:GDash
	RSU: 1CPN
		601: still creating images
		have images for kinking analysis
		
	Deonte

	TcB:

Funding:




**********************
Group meeting 6/26
****************
Bishop is in full proposal mode

SW: deonte is setup w/ Amber18/19
	its done
	Also got apache, nanocar js stuff running
	but not sure if NAMD/VMD/Amber/SQM are running on his laptop
	also don't know about django and other stuff

	zilong please make sure he sees the django simple app from John Gentle
	ran please make sure VMD/namd/SQM really work for him.

Let's encryp rally works and is CRONNed on DNA

SCIENCE CALENDARS:
RSU: ibiomes revision is not happening until  after 601
	ask for extension from JCIM until august

	601 need finalize figures using hte kinking count analysis

	working on it/discussed and have ideas

ZLI:  
	1CPN: looping  w/ lammps and 1CPN
	/autotmb/home/tmbshare/Public/Projects/1cpn/example-restrain-zilong
	has a trajectory of uniform 30nm w/ two clustes 3nucs on each end being 
	"fix drag" to a locaiton in space
	/autotmb/home/tmbshare/Public/Projects/1cpn/example-indent
	uses "fix indent" to try a smooth deformation		

	focus on python modules for G-Dash
	see 	/autotmb/home/zli007/Public/gdashstructure.odp