GMX-ANALYZE(1) GROMACS GMX-ANALYZE(1) NAME gmx-analyze - Analyze data sets SYNOPSIS gmx analyze [-f [<.xvg>]] [-ac [<.xvg>]] [-msd [<.xvg>]] [-cc [<.xvg>]] [-dist [<.xvg>]] [-av [<.xvg>]] [-ee [<.xvg>]] [-fitted [<.xvg>]] [-g [<.log>]] [-[no]w] [-xvg <enum>] [-[no]time] [-b <real>] [-e <real>] [-n <int>] [-[no]d] [-bw <real>] [-errbar <enum>] [-[no]integrate] [-aver_start <real>] [-[no]xydy] [-[no]regression] [-[no]luzar] [-temp <real>] [-fitstart <real>] [-fitend <real>] [-filter <real>] [-[no]power] [-[no]subav] [-[no]oneacf] [-acflen <int>] [-[no]normalize] [-P <enum>] [-fitfn <enum>] [-beginfit <real>] [-endfit <real>] DESCRIPTION gmx analyze reads an ASCII file and analyzes data sets. A line in the in- put file may start with a time (see option -time) and any number of y-val- ues may follow. Multiple sets can also be read when they are separated by & (option -n); in this case only one y-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 -d). All options, except for -av and -power, assume that the points are equidis- tant in time. gmx analyze 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 -ac produces the autocorrelation function(s). Be sure that the time interval between data points is much shorter than the time scale of the au- tocorrelation. Option -cc plots the resemblance of set i with a cosine of i/2 periods. The formula is: 2 (integral from 0 to T of y(t) cos(i pi t) dt)^2 / integral from 0 to T of y^2(t) dt This is useful for principal components obtained from covariance analysis, since the principal components of random diffusion are pure cosines. Option -msd produces the mean square displacement(s). Option -dist produces distribution plot(s). Option -av produces the average over the sets. Error bars can be added with the option -errbar. The errorbars can represent the standard devia- tion, the error (assuming the points are independent) or the interval con- taining 90% of the points, by discarding 5% of the points at the top and the bottom. Option -ee produces error estimates using block averaging. A set is di- vided in a number of blocks and averages are calculated for each block. The error for the total average is calculated from the variance between aver- ages of the m blocks B_i as follows: error^2 = 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 autocorre- lation is a sum of two exponentials. The analytical curve for the block average is: f(t) = sigma``*``sqrt(2/T ( alpha (tau_1 ((exp(-t/tau_1) - 1) tau_1/t + 1)) + (1-alpha) (tau_2 ((exp(-t/tau_2) - 1) tau_2/t + 1)))), where T is the total time. alpha, tau_1 and tau_2 are obtained by fitting f^2(t) to error^2. When the actual block average is very close to the ana- lytical curve, the error is sigma``*``sqrt(2/T (a tau_1 + (1-a) tau_2)). The complete derivation is given in B. Hess, J. Chem. Phys. 116:209-217, 2002. Option -filter prints the RMS high-frequency fluctuation of each set and over all sets with respect to a filtered average. The filter is propor- tional to cos(pi t/len) where t goes from -len/2 to len/2. len is supplied with the option -filter. This filter reduces oscillations with period len/2 and len by a factor of 0.79 and 0.33 respectively. Option -g fits the data to the function given with option -fitfn. Option -power fits the data to b t^a, 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 -luzar performs a Luzar & Chandler kinetics analysis on output from gmx hbond. The input file can be taken directly from gmx hbond -ac, and then the same result should be produced. Option -fitfn performs curve fitting to a number of different curves that make sense in the context of molecular dynamics, mainly exponential curves. More information is in the manual. To check the output of the fitting pro- cedure the option -fitted will print both the original data and the fitted function to a new data file. The fitting parameters are stored as comment in the output file. OPTIONS Options to specify input files: -f [<.xvg>] (graph.xvg) xvgr/xmgr file Options to specify output files: -ac [<.xvg>] (autocorr.xvg) (Optional) xvgr/xmgr file -msd [<.xvg>] (msd.xvg) (Optional) xvgr/xmgr file -cc [<.xvg>] (coscont.xvg) (Optional) xvgr/xmgr file -dist [<.xvg>] (distr.xvg) (Optional) xvgr/xmgr file -av [<.xvg>] (average.xvg) (Optional) xvgr/xmgr file -ee [<.xvg>] (errest.xvg) (Optional) xvgr/xmgr file -fitted [<.xvg>] (fitted.xvg) (Optional) xvgr/xmgr file -g [<.log>] (fitlog.log) (Optional) Log file Other options: -[no]w (no) View output .xvg, .xpm, .eps and .pdb files -xvg <enum> (xmgrace) xvg plot formatting: xmgrace, xmgr, none -[no]time (yes) Expect a time in the input -b <real> (-1) First time to read from set -e <real> (-1) Last time to read from set -n <int> (1) Read this number of sets separated by & -[no]d (no) Use the derivative -bw <real> (0.1) Binwidth for the distribution -errbar <enum> (none) Error bars for -av: none, stddev, error, 90 -[no]integrate (no) Integrate data function(s) numerically using trapezium rule -aver_start <real> (0) Start averaging the integral from here -[no]xydy (no) Interpret second data set as error in the y values for integrating -[no]regression (no) Perform a linear regression analysis on the data. If -xydy is set a second set will be interpreted as the error bar in the Y value. Oth- erwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi^2 = (y - A_0 x_0 - A_1 x_1 - ... - A_N x_N)^2 where now Y is the first data set in the input file and x_i the others. Do read the information at the option -time. -[no]luzar (no) Do a Luzar and Chandler analysis on a correlation function and re- lated as produced by gmx hbond. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). -temp <real> (298.15) Temperature for the Luzar hydrogen bonding kinetics analysis (K) -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 -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 -gem -filter <real> (0) Print the high-frequency fluctuation after filtering with a cosine filter of this length -[no]power (no) Fit data to: b t^a -[no]subav (yes) Subtract the average before autocorrelating -[no]oneacf (no) Calculate one ACF over all sets -acflen <int> (-1) Length of the ACF, default is half the number of frames -[no]normalize (yes) Normalize ACF -P <enum> (0) Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3 -fitfn <enum> (none) Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9 -beginfit <real> (0) Time where to begin the exponential fit of the correlation function -endfit <real> (-1) Time where to end the exponential fit of the correlation function, -1 is until the end SEE ALSO gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>. COPYRIGHT 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-ANALYZE(1)
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