GMX-ANALYZE(1) | GROMACS | GMX-ANALYZE(1) |

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>]

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

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)))),

**-f**[<.xvg>] (graph.xvg)- xvgr/xmgr file

**-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

**-[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. Otherwise, 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 related 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

September 15, 2017 | 2016.4 |