There are three ORAC input/output files in this dir.

popc.in: a simple example input file for running a short conventional
         NPT popc system simulation.  In order to produce the
         corresponding popc.out issue the command
	 
	 $ ORAC_DIR/orac < popc.in > mine_popc.out
	 Corresponding output is popc.out 

rem1.in : a sample REM starting input file based on lipid torsional
          tempering. The initial scaling protocol is defined in the
          file REM.set in this dir.  if REM.set is not present, the
          default scaling protocol is used (see manual).  In order to
          run this input issue the command
	  
          $ mpirun -n 24 $ORAC_DIR_MPI/orac < rem1.in > rem1.out

          This command will produce in this dir 24 subdir, each
          containing the data from one single GE walker. More info on
          HREM setup can be found in the rem1.in file Corresponding
          output(standard) is rem1.out


rem2.in : a sample REM input file for *restarting* the lipid torsional
          tempering simulation. When restarting a rem simulation
          (rem2.in), the REM.set is read form the PARxxxx dirs.  In
          order to run this input issue the command

          $  mpirun -n 24 $ORAC_DIR_MPI/orac < rem2.in > rem2.out
	   
          More info on a restarted (continued) HREM simulation can be
          found in the rem2.in file Corresponding output(standard) is
          rem2.out



The 24 PARxxxx directories are generated and filled by the running the two rem1.in and rem2.in
in sequence. The content of these directories must match that found in the directories
archived in the file REF.PAR.tar.bz2 available at www.chim.unifi.it/orac

After running the examples each of the 24 PARxxxx dir should contain:


PAR0001/popc2.rst      ! the restart file run #2  
PAR0001/popc1.rst      ! the restart file run #1

# for run #n only the #(n-1) file should be kept.   

PAR0001/2.rem          ! time record of the unscaled energies of run #2 
PAR0001/1.rem          ! time record of the unscaled energies of run #1

# these files must be kept for later MBAR weights for all GE configurations 


PAR0001/popc_t2.pdb     ! pdb file of the full system run #2 
PAR0001/popc_t1.pdb     ! pdb file of the full system run #1 


PAR0001/REM.set          ! scaling protocol

PAR0001/REM_DIAGNOSTIC   ! diagnostic file (overwritten at each restarted run )

PAR0001/INPUT            ! copy of input file 

PAR0001/out0001          ! output file (overwritten at each restarted run) 




