g_bar

Langue: en

Version: 371336 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)

NAME

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

VERSION 4.5

SYNOPSIS

g_bar -f dhdl.xvg -o bar.xvg -oi barint.xvg -oh histogram.xvg -g energy.edr -[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. Input option -f expects multiple dhdl 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 Delta lambda. The lambda values are inferred from the legends: lambda of the simulation from the legend of dH/dlambda and the foreign lambda's 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's from the legend containing the capitalized letters 'D' and 'H'. The temperature is parsed from the legend line containing 'T ='.

The free energy estimates are determined using BAR with bisection, the precision of the output is 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 blocks numbers for error estimation can be provided with the options -nbmin and -nbmax.

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 (2009) 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 gives an estimate of the quality of sampling (not directly of the actual statistical error, because it assumes independent samples).

FILES

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

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

OTHER OPTIONS

-[no]hno
 Print help info and quit

-[no]versionno
 Print version info and quit

-nice int 0
 Set the nicelevel

-[no]wno
 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

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.