g_bar(1) - f14

1g_bar(1)                  GROMACS suite, VERSION 4.5                  g_bar(1)
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NAME

6       g_bar  -  calculates free energy difference estimates through Bennett's
7       acceptance ratio
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9       VERSION 4.5
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SYNOPSIS

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

17       g_bar calculates free energy  difference  estimates  through  Bennett's
18       acceptance ratio method.  Input option  -f expects multiple dhdl files.
19       Two types of input files are supported:
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21       * Files with only one y-value, for such files it is  assumed  that  the
22       y-value  is  dH/dlambda  and  that  the Hamiltonian depends linearly on
23       lambda. The lambda value of the simulation is inferred from the  subti‐
24       tle if present, otherwise from a number in the subdirectory in the file
25       name.
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27       * Files with more than one y-value. The files should have columns  with
28       dH/dlambda  and  Delta  lambda. The lambda values are inferred from the
29       legends: lambda of the simulation from the legend of dH/dlambda and the
30       foreign lambda's from the legends of Delta H.
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33       The lambda of the simulation is parsed from dhdl.xvg file's legend con‐
34       taining the string 'dH', the foreign lambda's from the legend  contain‐
35       ing the capitalized letters 'D' and 'H'. The temperature is parsed from
36       the legend line containing 'T ='.
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39       The free energy estimates are determined using BAR with bisection,  the
40       precision  of  the output is set with  -prec.  An error estimate taking
41       into account time correlations is  made  by  splitting  the  data  into
42       blocks  and  determining  the free energy differences over those blocks
43       and assuming the blocks are independent.  The final error  estimate  is
44       determined  from  the average variance over 5 blocks. A range of blocks
45       numbers for error estimation can be provided with the  options   -nbmin
46       and  -nbmax.
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49       The  results  are  split in two parts: the last part contains the final
50       results in kJ/mol, together with the error estimate for each  part  and
51       the  total.  The  first  part  contains detailed free energy difference
52       estimates and phase space overlap measures in  units  of  kT  (together
53       with their computed error estimate). The printed values are:
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55       *  lam_A: the lambda values for point A.
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57       *  lam_B: the lambda values for point B.
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59       *     DG: the free energy estimate.
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61       *    s_A: an estimate of the relative entropy of B in A.
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63       *    s_A: an estimate of the relative entropy of A in B.
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65       *  stdev: an estimate expected per-sample standard deviation.
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68       The  relative  entropy  of  both states in each other's ensemble can be
69       interpreted as a measure of phase space overlap: the  relative  entropy
70       s_A  of  the  work samples of lambda_B in the ensemble of lambda_A (and
71       vice versa for s_B), is a measure of the 'distance'  between  Boltzmann
72       distributions  of  the two states, that goes to zero for identical dis‐
73       tributions. See Wu & Kofke, J. Chem. Phys. 123 084109 (2009)  for  more
74       information.
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77       The estimate of the expected per-sample standard deviation, as given in
78       Bennett's original BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976),
79       Eq.  10  gives  an estimate of the quality of sampling (not directly of
80       the actual statistical error, because it assumes independent samples).
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FILES

85       -f dhdl.xvg Input, Opt., Mult.
86        xvgr/xmgr file
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88       -o bar.xvg Output, Opt.
89        xvgr/xmgr file
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91       -oi barint.xvg Output, Opt.
92        xvgr/xmgr file
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94       -oh histogram.xvg Output, Opt.
95        xvgr/xmgr file
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97       -g energy.edr Input, Opt., Mult.
98        Energy file
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OTHER OPTIONS

102       -[no]hno
103        Print help info and quit
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105       -[no]versionno
106        Print version info and quit
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108       -nice int 0
109        Set the nicelevel
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111       -[no]wno
112        View output xvg, xpm, eps and pdb files
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114       -xvg enum xmgrace
115        xvg plot formatting:  xmgrace,  xmgr or  none
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117       -b real 0
118        Begin time for BAR
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120       -e real -1
121        End time for BAR
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123       -temp real -1
124        Temperature (K)
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126       -prec int 2
127        The number of digits after the decimal point
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129       -nbmin int 5
130        Minimum number of blocks for error estimation
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132       -nbmax int 5
133        Maximum number of blocks for error estimation
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135       -nbin int 100
136        Number of bins for histogram output
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO