Provided by: gromacs-data_4.6.5-1build1_all bug


       g_bar - calculates free energy difference estimates through Bennett's acceptance ratio

       VERSION 4.6.5


       g_bar  -f  dhdl.xvg  -g  ener.edr  -o  bar.xvg  -oi  barint.xvg  -oh  histogram.xvg -[no]h
       -[no]version -nice int -[no]w -xvg enum -b real -e real -temp real -prec  int  -nbmin  int
       -nbmax int -nbin int -[no]extp


         g_bar  calculates  free  energy  difference estimates through Bennett's acceptance ratio
       method (BAR). It also automatically adds series of individual free energies obtained  with
       BAR into a combined free energy estimate.

       Every individual BAR free energy difference relies on two simulations at different states:
       say state A and state B, as controlled by a parameter, lambda (see the   .mdp  parameter
       init_lambda).  The  BAR  method  calculates a ratio of weighted average of the Hamiltonian
       difference of state B given state A and vice versa.  The energy differences to  the  other
       state must be calculated explicitly during the simulation. This can be done with the  .mdp
       option  foreign_lambda.

       Input option  -f  expects  multiple   dhdl.xvg  files.   Two  types  of  input  files  are

         *  Files with more than one  y-value.  The files should have columns with dH/dlambda and
       Deltalambda.  The lambda values are inferred from the legends: lambda  of  the  simulation
       from the legend of dH/dlambda and the foreign lambda values from the legends of Delta H

         *   Files with only one  y-value. Using the  -extp option for these files, it is assumed
       that the  y-value is dH/dlambda and that the Hamiltonian depends linearly on lambda.   The
       lambda  value of the simulation is inferred from the subtitle (if present), otherwise from
       a number in the subdirectory in the file name.

       The lambda of the simulation is parsed from  dhdl.xvg file's legend containing the  string
       'dH', the foreign lambda values from the legend containing the capitalized letters 'D' and
       'H'. The temperature is parsed from the legend line containing 'T ='.

       The input option  -g expects multiple  .edr files.  These  can  contain  either  lists  of
       energy  differences  (see the  .mdp option  separate_dhdl_file), or a series of histograms
       (see the  .mdp options  dh_hist_size and  dh_hist_spacing).  The  temperature  and  lambda
       values are automatically deduced from the  ener.edr file.

       In  addition  to  the   .mdp  option   foreign_lambda,  the  energy difference can also be
       extrapolated from the dH/dlambda values. This is done with the -extp option, which assumes
       that the system's Hamiltonian depends linearly on lambda, which is not normally the case.

       The  free  energy estimates are determined using BAR with bisection, with the precision of
       the output set with  -prec.  An error estimate taking into account  time  correlations  is
       made  by  splitting  the data into blocks and determining the free energy differences over
       those blocks and assuming the  blocks  are  independent.   The  final  error  estimate  is
       determined  from  the  average  variance over 5 blocks. A range of block numbers for error
       estimation can be provided with the options  -nbmin and  -nbmax.

        g_bar tries to aggregate samples with the same 'native' and 'foreign' lambda values,  but
       always    assumes    independent    samples.     Note   that   when   aggregating   energy
       differences/derivatives with different sampling intervals, this is  almost  certainly  not
       correct.  Usually  subsequent  energies  are  correlated and different time intervals mean
       different degrees of correlation between samples.

       The results are split in two parts: the last part contains the final  results  in  kJ/mol,
       together  with  the  error  estimate  for each part and the total. The first part contains
       detailed free energy difference estimates and phase space overlap measures in units of  kT
       (together with their computed error estimate). The printed values are:

        *  lam_A: the lambda values for point A.

        *  lam_B: the lambda values for point B.

        *     DG: the free energy estimate.

        *    s_A: an estimate of the relative entropy of B in A.

        *    s_B: an estimate of the relative entropy of A in B.

        *  stdev: an estimate expected per-sample standard deviation.

       The  relative  entropy  of  both  states  in each other's ensemble can be interpreted as a
       measure of phase space overlap: the relative entropy s_A of the work samples  of  lambda_B
       in  the  ensemble  of  lambda_A  (and  vice versa for s_B), is a measure of the 'distance'
       between Boltzmann distributions of the  two  states,  that  goes  to  zero  for  identical
       distributions. See Wu & Kofke, J. Chem. Phys. 123 084109 (2005) for more information.

       The estimate of the expected per-sample standard deviation, as given in Bennett's original
       BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976).  Eq. 10 therein gives an estimate  of
       the  quality of sampling (not directly of the actual statistical error, because it assumes
       independent samples).

       To get a visual estimate of the phase space overlap, use the  -oh option to  write  series
       of histograms, together with the  -nbin option.


       -f dhdl.xvg Input, Opt., Mult.
        xvgr/xmgr file

       -g ener.edr Input, Opt., Mult.
        Energy file

       -o bar.xvg Output, Opt.
        xvgr/xmgr file

       -oi barint.xvg Output, Opt.
        xvgr/xmgr file

       -oh histogram.xvg Output, Opt.
        xvgr/xmgr file


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -b real 0
        Begin time for BAR

       -e real -1
        End time for BAR

       -temp real -1
        Temperature (K)

       -prec int 2
        The number of digits after the decimal point

       -nbmin int 5
        Minimum number of blocks for error estimation

       -nbmax int 5
        Maximum number of blocks for error estimation

       -nbin int 100
        Number of bins for histogram output

        Whether to linearly extrapolate dH/dl values to use as energies



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                 g_bar(1)