Input example for the program mbar.

syntax:  mbar PARAMETER_FILE DATA_FILE [guess [debug]] 

where 

**** PARAMETER_FILE is the file containing the scaling factors
     for H-REM. It contains as many lines as replicas. 
     The format of file is, e.g., 
#   c_1             c_2
1.00000000000000 1.0000000000000
0.97788853633543 1.0058986695810
0.95626598949625 1.0118321334648
0.93512154881584 1.0178005968916
0.91444464266725 1.0238042663120
0.89422493317765 1.0298433493947
0.87445231105974 1.0359180550330
0.85511689055735 1.0420285933526
0.83620900450283 1.0481751757188
....
.... 

     where c_1 and c_2 are the components of the scaling vector and
     each line refers to a replica.  This input PARAMETER_FILE file
     for mbar can be generated from the ORAC REM.set with the command

$ awk '{if($1 ~ "[0-9]" ) print $2, $3,$4}' PAR0000/REM.set > PARAMETER_FILE

     http://www.chim.unifi.it/orac  for documentation on the ORAC code.

**** DATA_FILE is the file containing the energies sampled in the
     H-REM simulation in RT units (T is the the temperature of the
     H-REM GE).  If the operating temperature in the GE is, e.g., 300
     K, this mbar input file can be generated for the energy file
     produced by the ORAC code (http://www.chim.unifi.it/orac) using
     the command:
  
awk '{print $2, $3/2.4942, $4/2.4942, $5/2.4942}' energy_file > mbar.dat

     N.B.: The program assumes that an equal number of configurations
     are sampled in each replica.  The format is the following:

# Nrep     v_1         v_2
   1     1862.72     -1790.96
   1     1892.21     -1832.87
   2     1875.37     -1836.45
   1     1899.11     -1816.16
   2     1885.64     -1810.15
   3     1897.09     -1792.71
   1     1852.37     -1838
   1     1913.79     -1807.6
...
...

    For each line, the first integer labels the replica-state k. The
    two real numbers are the (unscaled) energy v_1 and v_2 (in RT
    units) sampled in the k state.

**** guess: if (guess == "T") the the BAR initial guess for the Z_k is used.


**** debug: if (debug == "T") then the (unscaled) energy distributions
     for each replica are printed out in the DISTRIBUTIONS directory.
     convergence info is also printed out to Std-err.

     Use the command 

$ mbar PARAMETER_FILE DATA_FILE T T 

     to produce a verbose output using the BAR initial guess for the
     partition functions Z_k.

**** weights for each GE point whose (unscaled) energies are specified
     in DATA_FILE are printed to StOUT.
