.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_analyze - analyzes data sets .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_analyze\fP .BI "\-f" " graph.xvg " .BI "\-ac" " autocorr.xvg " .BI "\-msd" " msd.xvg " .BI "\-cc" " coscont.xvg " .BI "\-dist" " distr.xvg " .BI "\-av" " average.xvg " .BI "\-ee" " errest.xvg " .BI "\-bal" " ballisitc.xvg " .BI "\-g" " fitlog.log " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-[no]time" "" .BI "\-b" " real " .BI "\-e" " real " .BI "\-n" " int " .BI "\-[no]d" "" .BI "\-bw" " real " .BI "\-errbar" " enum " .BI "\-[no]integrate" "" .BI "\-aver_start" " real " .BI "\-[no]xydy" "" .BI "\-[no]regression" "" .BI "\-[no]luzar" "" .BI "\-temp" " real " .BI "\-fitstart" " real " .BI "\-fitend" " real " .BI "\-smooth" " real " .BI "\-filter" " real " .BI "\-[no]power" "" .BI "\-[no]subav" "" .BI "\-[no]oneacf" "" .BI "\-acflen" " int " .BI "\-[no]normalize" "" .BI "\-P" " enum " .BI "\-fitfn" " enum " .BI "\-ncskip" " int " .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION \&\fB g_analyze\fR reads an ASCII file and analyzes data sets. \&A line in the input file may start with a time \&(see option \fB \-time\fR) and any number of \fI y\fR\-values may follow. \&Multiple sets can also be \&read when they are separated by & (option \fB \-n\fR); \&in this case only one \fI y\fR\-value is read from each line. \&All lines starting with and @ are skipped. \&All analyses can also be done for the derivative of a set \&(option \fB \-d\fR). \&All options, except for \fB \-av\fR and \fB \-power\fR, assume that the \&points are equidistant in time. \&\fB g_analyze\fR always shows the average and standard deviation of each \&set, as well as the relative deviation of the third \&and fourth cumulant from those of a Gaussian distribution with the same \&standard deviation. \&Option \fB \-ac\fR produces the autocorrelation function(s). \&Option \fB \-cc\fR plots the resemblance of set i with a cosine of \&i/2 periods. The formula is: 2 (int0\-T y(t) cos(i pi t) dt)2 / int0\-T y(t) y(t) dt \&This is useful for principal components obtained from covariance \&analysis, since the principal components of random diffusion are \&pure cosines. \&Option \fB \-msd\fR produces the mean square displacement(s). \&Option \fB \-dist\fR produces distribution plot(s). \&Option \fB \-av\fR produces the average over the sets. \&Error bars can be added with the option \fB \-errbar\fR. \&The errorbars can represent the standard deviation, the error \&(assuming the points are independent) or the interval containing \&90% of the points, by discarding 5% of the points at the top and \&the bottom. \&Option \fB \-ee\fR produces error estimates using block averaging. \&A set is divided in a number of blocks and averages are calculated for \&each block. The error for the total average is calculated from \&the variance between averages of the m blocks B_i as follows: \&error2 = Sum (B_i \- B)2 / (m*(m\-1)). \&These errors are plotted as a function of the block size. \&Also an analytical block average curve is plotted, assuming \&that the autocorrelation is a sum of two exponentials. \&The analytical curve for the block average is: \&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) + \& (1\-alpha) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))), where T is the total time. \&alpha, tau1 and tau2 are obtained by fitting f2(t) to error2. \&When the actual block average is very close to the analytical curve, \&the error is sigma\fB *\fRsqrt(2/T (a tau1 + (1\-a) tau2)). \&The complete derivation is given in \&B. Hess, J. Chem. Phys. 116:209\-217, 2002. \&Option \fB \-bal\fR finds and subtracts the ultrafast "ballistic" \&component from a hydrogen bond autocorrelation function by the fitting \&of a sum of exponentials, as described in e.g. \&O. Markovitch, J. Chem. Phys. 129:084505, 2008. The fastest term \&is the one with the most negative coefficient in the exponential, \&or with \fB \-d\fR, the one with most negative time derivative at time 0. \&\fB \-nbalexp\fR sets the number of exponentials to fit. \&Option \fB \-gem\fR fits bimolecular rate constants ka and kb \&(and optionally kD) to the hydrogen bond autocorrelation function \&according to the reversible geminate recombination model. Removal of \&the ballistic component first is strongly advised. The model is presented in \&O. Markovitch, J. Chem. Phys. 129:084505, 2008. \&Option \fB \-filter\fR prints the RMS high\-frequency fluctuation \&of each set and over all sets with respect to a filtered average. \&The filter is proportional to cos(pi t/len) where t goes from \-len/2 \&to len/2. len is supplied with the option \fB \-filter\fR. \&This filter reduces oscillations with period len/2 and len by a factor \&of 0.79 and 0.33 respectively. \&Option \fB \-g\fR fits the data to the function given with option \&\fB \-fitfn\fR. \&Option \fB \-power\fR fits the data to b ta, which is accomplished \&by fitting to a t + b on log\-log scale. All points after the first \&zero or with a negative value are ignored. Option \fB \-luzar\fR performs a Luzar & Chandler kinetics analysis \&on output from \fB g_hbond\fR. The input file can be taken directly \&from \fB g_hbond \-ac\fR, and then the same result should be produced. .SH FILES .BI "\-f" " graph.xvg" .B Input xvgr/xmgr file .BI "\-ac" " autocorr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-msd" " msd.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-cc" " coscont.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-dist" " distr.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-av" " average.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ee" " errest.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-bal" " ballisitc.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-g" " fitlog.log" .B Output, Opt. Log 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 "\-[no]time" "yes " Expect a time in the input .BI "\-b" " real" " \-1 " First time to read from set .BI "\-e" " real" " \-1 " Last time to read from set .BI "\-n" " int" " 1" Read sets separated by & .BI "\-[no]d" "no " Use the derivative .BI "\-bw" " real" " 0.1 " Binwidth for the distribution .BI "\-errbar" " enum" " none" Error bars for \fB \-av\fR: \fB none\fR, \fB stddev\fR, \fB error\fR or \fB 90\fR .BI "\-[no]integrate" "no " Integrate data function(s) numerically using trapezium rule .BI "\-aver_start" " real" " 0 " Start averaging the integral from here .BI "\-[no]xydy" "no " Interpret second data set as error in the y values for integrating .BI "\-[no]regression" "no " Perform a linear regression analysis on the data. If \fB \-xydy\fR is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi2 = (y \- A0 x0 \- A1 x1 \- ... \- AN xN)2 where now Y is the first data set in the input file and xi the others. Do read the information at the option \fB \-time\fR. .BI "\-[no]luzar" "no " Do a Luzar and Chandler analysis on a correlation function and related as produced by \fB g_hbond\fR. When in addition the \fB \-xydy\fR flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). .BI "\-temp" " real" " 298.15" Temperature for the Luzar hydrogen bonding kinetics analysis .BI "\-fitstart" " real" " 1 " Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation .BI "\-fitend" " real" " 60 " Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with \fB \-gem\fR .BI "\-smooth" " real" " \-1 " If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau) .BI "\-filter" " real" " 0 " Print the high\-frequency fluctuation after filtering with a cosine filter of length .BI "\-[no]power" "no " Fit data to: b ta .BI "\-[no]subav" "yes " Subtract the average before autocorrelating .BI "\-[no]oneacf" "no " Calculate one ACF over all sets .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames .BI "\-[no]normalize" "yes " Normalize ACF .BI "\-P" " enum" " 0" Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions .BI "\-beginfit" " real" " 0 " Time where to begin the exponential fit of the correlation function .BI "\-endfit" " real" " \-1 " Time where to end the exponential fit of the correlation function, \-1 is until the end .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.