.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_bar - calculates free energy difference estimates through Bennett's acceptance ratio .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_bar\fP .BI "\-f" " dhdl.xvg " .BI "\-g" " ener.edr " .BI "\-o" " bar.xvg " .BI "\-oi" " barint.xvg " .BI "\-oh" " histogram.xvg " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-b" " real " .BI "\-e" " real " .BI "\-temp" " real " .BI "\-prec" " int " .BI "\-nbmin" " int " .BI "\-nbmax" " int " .BI "\-nbin" " int " .SH DESCRIPTION \&\fB g_bar\fR 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 \fB .mdp\fR parameter \&\fB init_lambda\fR). 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 \fB free_energy\fR is on), \&the energy differences to the other state need to be calculated \&explicitly during the simulation. This can be controlled with \&the \fB .mdp\fR option \fB foreign_lambda\fR. \&Input option \fB \-f\fR expects multiple \fB dhdl.xvg\fR files. \&Two types of input files are supported: \&\fB *\fR Files with only one \fI y\fR\-value, for such files it is assumed \& that the \fI y\fR\-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. \& \&\fB *\fR Files with more than one \fI y\fR\-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 \fB dhdl.xvg\fR 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 \fB \-g\fR expects multiple \fB .edr\fR files. \&These can contain either lists of energy differences (see the \&\fB .mdp\fR option \fB separate_dhdl_file\fR), or a series of histograms \&(see the \fB .mdp\fR options \fB dh_hist_size\fR and \fB dh_hist_spacing\fR). \&The temperature and lambda values are automatically deduced from \&the \fB ener.edr\fR file. The free energy estimates are determined using BAR with bisection, \&with the precision of the output set with \fB \-prec\fR. \&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 \fB \-nbmin\fR and \fB \-nbmax\fR. \&\fB g_bar\fR tries to aggregate samples with the same 'native' and 'foreign' \&lambda values, but always assumes independent samples. \fB Note\fR 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: \&\fB *\fR lam_A: the lambda values for point A. \&\fB *\fR lam_B: the lambda values for point B. \&\fB *\fR DG: the free energy estimate. \&\fB *\fR s_A: an estimate of the relative entropy of B in A. \&\fB *\fR s_A: an estimate of the relative entropy of A in B. \&\fB *\fR 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 \&\fB \-oh\fR option to write series of histograms, together with the \&\fB \-nbin\fR option. .SH FILES .BI "\-f" " dhdl.xvg" .B Input, Opt., Mult. xvgr/xmgr file .BI "\-g" " ener.edr" .B Input, Opt., Mult. Energy file .BI "\-o" " bar.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oi" " barint.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-oh" " histogram.xvg" .B Output, Opt. xvgr/xmgr file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-[no]w" "no " View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-b" " real" " 0 " Begin time for BAR .BI "\-e" " real" " \-1 " End time for BAR .BI "\-temp" " real" " \-1 " Temperature (K) .BI "\-prec" " int" " 2" The number of digits after the decimal point .BI "\-nbmin" " int" " 5" Minimum number of blocks for error estimation .BI "\-nbmax" " int" " 5" Maximum number of blocks for error estimation .BI "\-nbin" " int" " 100" Number of bins for histogram output .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.