         *************************************************
	 * TESTS FOR ALCHEMICAL TRANSFORMATION WITH ORAC *
         *************************************************

This README decuments the regular, non-parallel ("serial")
implementation of alchemical transformation MD (see [1],[2]) in ORAC

For the parallel implementation of alchemical transformation MD, see
README_PARALLEL

----
[1] W.L. Joergensen et al., J. Chem. Phys. 85 (1985), 3050

[2] M.R. Shirts et al., Annual Reports in Computational Chemistry
3(2007), 41

------------------------------------------------------------------------
BEFORE RUNNING THE TESTS
------------------------------------------------------------------------

* Build the appropriate executable of the ORAC program, e.g. :

   cd <orac6-root-dir>
   ./configure -INTEL -FFTW -OMP -MPI
   make   ! create an hybrid OMP/MPI executable in  INTEL-FFTW-OMP-MPI dir    
   ./configure -INTEL -FFTW -OMP 
   make  ! create an hybrid OMP executable in  INTEL-FFTW-OMP dir    

* Adjust the variables in the first section of ./Makefile :

  O_BIN

and possibly

  O_ROOT 
  O_SRC  
  ORAC   


------------------------------------------------------------------------
TO RUN THE TESTS
------------------------------------------------------------------------

Tests are preferably run through `make'.


* to run all the serial tests in sequence:

  `make'
  
  this will run the script `run_serial_tests.bash' from this
  directory, which in turn will call the following scripts:

    forward_trajectories.bash
	script for producing non equilibrium forward trajectories

    reverse_trajectories.bash 
	script for producing non equilibrium reverse trajectories

  as well as the ancillary program 

    bennett
        (see ${O_ROOT}/tools/bennett for more info)
  

* to run individual tests (for example):

   `make 2.out'



The tests will create several output files, and a collection of
selected output lines in OUT_TEST; this file is to be compared to
the reference file OUT.

NOTE that even small differences of numerical origin will soon drive a
trajectory away from the reference path. Thus, the work distribution
may differ significantly from the reference data.
 

------------------------------------------------------------------------
SHORT DESCRIPTION OF TESTS
------------------------------------------------------------------------

- Please read the manual ( ${O_ROOT}/doc/orac-manual.pdf ) for a
  detailed description of the program and its input


1.in + 1r.in : produce one work calculation for the switch-ON process
               of N-Elte378 in hexane

2.in + 2r.in : produce one work calculation for the switch-OFF process
               of N-Elte378 in hexane

3.in + 3r.in : produce one work calculation for the switch-ON of one
       	       N-Elte378 molecule and the concurrent switch-OFF of a
       	       second N-Elte378 molecule in hexane
