Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_analyze - analyzes data sets
VERSION 4.6.5
SYNOPSIS
g_analyze -f graph.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -dist distr.xvg -av average.xvg -ee
errest.xvg -bal ballisitc.xvg -g fitlog.log -[no]h -[no]version -nice int -[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 -smooth real -filter real -[no]power
-[no]subav -[no]oneacf -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit
real
DESCRIPTION
g_analyze reads an ASCII file and analyzes data sets. A line in the input file may start with a time
(see option -time) and any number of y-values 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 equidistant in time.
g_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 autocorrelation.
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 y2(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 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 -ee 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 *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 f2(t) to error2. When the actual block average is very
close to the analytical 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 -bal 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 -d, the one with most negative time derivative at time 0. -nbalexp sets the number of
exponentials to fit.
Option -gem 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 -filter 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 -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 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 -luzar performs a Luzar & Chandler kinetics analysis on output from g_hbond. The input file can
be taken directly from g_hbond -ac, and then the same result should be produced.
FILES
-f graph.xvg Input
xvgr/xmgr file
-ac autocorr.xvg Output, Opt.
xvgr/xmgr file
-msd msd.xvg Output, Opt.
xvgr/xmgr file
-cc coscont.xvg Output, Opt.
xvgr/xmgr file
-dist distr.xvg Output, Opt.
xvgr/xmgr file
-av average.xvg Output, Opt.
xvgr/xmgr file
-ee errest.xvg Output, Opt.
xvgr/xmgr file
-bal ballisitc.xvg Output, Opt.
xvgr/xmgr file
-g fitlog.log Output, Opt.
Log 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
-[no]timeyes
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]dno
Use the derivative
-bw real 0.1
Binwidth for the distribution
-errbar enum none
Error bars for -av: none, stddev, error or 90
-[no]integrateno
Integrate data function(s) numerically using trapezium rule
-aver_start real 0
Start averaging the integral from here
-[no]xydyno
Interpret second data set as error in the y values for integrating
-[no]regressionno
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. Otherwise, if multiple data sets are present a multilinear regression will
be performed yielding the constant A that minimize chi2 = (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]luzarno
Do a Luzar and Chandler analysis on a correlation function and related as produced by g_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
-smooth real -1
If this value is = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y =
A exp(-x/tau)
-filter real 0
Print the high-frequency fluctuation after filtering with a cosine filter of this length
-[no]powerno
Fit data to: b ta
-[no]subavyes
Subtract the average before autocorrelating
-[no]oneacfno
Calculate one ACF over all sets
-acflen int -1
Length of the ACF, default is half the number of frames
-[no]normalizeyes
Normalize ACF
-P enum 0
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
-fitfn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-ncskip int 0
Skip this many points in the output file of correlation functions
-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
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 2 Dec 2013 g_analyze(1)