ADK
====

Data generated with CHARMM:
  closed/
  open/

Molecule adk.closed has been reoriented by minimizing
the root mean square difference between open en closed form.
Input files *.inp
Output files *.out


Analysis is bases on the script:
  analyse-adk.py

Blocks and Subsystem
^^^^^^^^^^^^^^^^^^^^
python script.generatefixed.py  --  to generate the block choices and
subsystem/environment divisions as described below


FULL
^^^^
./script.full.open  --  to launch the NMA calculation
./script.full.closed  --  to launch the NMA calculation

MBH
^^^
RTB blocks

1
2
3
4
5

MBH with adjoined blocks

11 RHbending  calpha belonging to 4 blocks
12 dihedral  only dihedral angles phi and psi
13 normal  calpha belonging to 3 blocks

./script.mbh.open  --  to launch the MBH NMA calculation
./script.mbh.closed  --  to launch the MBH NMA calculation

VSA
^^^
6
7
8
9
10

./script.vsa.open  --  to launch the VSA NMA calculation
./script.vsa.closed  --  to launch the VSA NMA calculation



Overlap delta vector
^^^^^^^^^^^^^^^^^^^^
cd output/

./script.overlap.full  --  to calculate the overlap between full Hessian modes and
the conformational change

./script.overlap  --  to calculate the overlap between approximate modes and
the conformational change

python get_overlap_7-7.py  --  to pick out the overlap of the lowest nonzero
mode and write the summary file delta.overlaps.7-7.csv


Free energy difference
^^^^^^^^^^^^^^^^^^^^^^

First increase the accuracy of the free energy output:
in file ..../tamkin/lib/tools.py
change the format e.g. from %f.1 to %f.5 for the energy etc.

cd output/

./script.gibbs  --  to construct the partition functions based on chk-files

./script.grep  --  to gather the information in a file thermo.all.csv
