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mention paths and extendnmr istallation notes
and also about working path (what we store there)

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To run ISD from Extend-NMR graphical user interface (GUI)
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* Open CCPN project:

  Extend-NMR GUI > Project > Open

* Now ISD tab of the GUI will contain default settings for 
  running ISD simulation.

* Usual steps needed to set up ISD simulation:

  1. Settings for the current ISD simulation will be saved in 
     the selected CCPN project under selected ISD storage key
     (define different storage keys for different 
      simulation settings):

     ISD > General > CCPN ISD Storage Key

     It is allowed to save several ISD project settings inside 
     CCPN project under different ISD storage keys. 

     ISD simulation settings can be saved or deleted with buttons
     "Save ISD settings" or "Delete ISD settings".

     You can select saved ISD settings from dropdown menu in the 
     top left corner of the ISD tab. 

  2. Check ISD working path that is where the ISD project 
     file and the results will be saved:

     ISD > General > ISD Working Path 

  3. Check the CCPN molecule settings (if there is only one molecule
     in the CCPN project, it will be selected by default):

     ISD > General > CCPN NMR Project ID
     ISD > General > CCPN Molecular System Name 
     ISD > Molecules & Structures > CCPN Molecule Key

  4. Select experimental data to be used in the simulation
     (e.g. distance):
     
     ISD > Experimental Data > Add Distance

     Select the field with the added data, and commit changes.

  5. Select the hosts on which simulation should be run:

     ISD > Replica Exchange MC > Host List

     Example: boar 10, localhost
              will use 10 CPUs on boar and 1 CPU on localhost
  
     The default method of communicating between
     different hosts is 'shared'. For more information, 
     please read notes below and the ISD manual.          

* Go through all the tables in ISD GUI and check the settings.

  NOTE: fields highlighted in red require attention

* Now you can start simulation by pressing "Run ISD!" button,
  stop it at any point with "Stop ISD!", monitor progress
  using "Info", "Show", "Energies", "Rates".

  To analyse the results of simulation use "Report" button.
 
  To create ISD project on disk (in ISD working path) use
  "Create" button.

  Once the project is created, it can be run from command
  line :

  % cd isd/working/path
  % $EXTEND_NMR_TOPDIR/bin/isd x.py

  To find help on command line options use (for more 
  information please read ISD manual):

  % $EXTEND_NMR_TOPDIR/bin/isd --help
  

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Prerequisites for running ISD simulation
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* Password free ssh access to the hosts on which ISD 
  will be running

* Python shipped with Extend-NMR on each of the hosts
  (it has all needed libraries such as numpy, PyRO, etc)

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Communication settings
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* Selecting communication method between hosts:

  ISD > Replica Exchange MC > Communication Method

  - select 'shared' if you use hosts that can specify folder 
    (shared temporary path used by ISD) to which all the hosts have
    read and write access

    E.g: select 'shared' if you run simulation on single 
         machine that has many CPUs

  - select 'pyro' if the machines cannot have shared
    temporary path

* When using 'shared' communication method, check following:

  ISD > Replica Exchange MC > Communication Method
  ISD > General > Temporary Path
  ISD > General > Shared Temporary Path?  <------ must be set to True
  ISD > Replica Exchange MC > Host List

* When using 'pyro' communication method, check following:

  1) Check general communication settings

  ISD > Replica Exchange MC > Communication Method
  ISD > General > Temporary Path
  ISD > General > Shared Temporary Path?  <------ can be set to False
  ISD > Replica Exchange MC > Host List  

  2) Make sure that PyRO nameserver is running: 

     To start PyRO nameserver run: 
     % $EXTEND_NMR_TOPDIR/bin/pyro-ns

     After the simulation is complete stop nameserver:
     % $EXTEND_NMR_TOPDIR/bin/pyro-nsc shutdown
 
  3) Make sure that the name of the machine running nameserver 
     is set up correctly:

     ISD > Replica Exchange MC > PyRO Name Server

  4) Make sure that every host listed has access to Python
     provided by Extend-NMR. The path to the Python 
     executable on the remote host is specified here:

     ISD > Replica Exchange MC > Python Binary


