## SYNOPSIS

**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*

## DESCRIPTION

**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. If the Hamiltonian does not depend linearly on lambda
(in which case we can extrapolate the derivative of the Hamiltonian
with respect to lambda, as is the default when ** free_energy** is on),
the energy differences to the other state need to be calculated
explicitly during the simulation. This can be controlled with
the ** .mdp** option ** foreign_lambda**.

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

** *** Files with only one * y*-value, for such 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.

** *** 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.

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.

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_A: 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.

## FILES

**-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

## OTHER OPTIONS

**-[no]h**

*no*

Print help info and quit

**-[no]version***no *

Print version info and quit

**-nice*** int*** 0**

Set the nicelevel

**-[no]w***no *

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