This is the command gmx-dielectric that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-dielectric - Calculate frequency dependent dielectric constants
SYNOPSIS
gmx dielectric [-f [<.xvg>]] [-d [<.xvg>]] [-o [<.xvg>]] [-c [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-[no]w]
[-xvg <enum>] [-[no]x1] [-eint <real>] [-bfit <real>]
[-efit <real>] [-tail <real>] [-A <real>] [-tau1 <real>]
[-tau2 <real>] [-eps0 <real>] [-epsRF <real>]
[-fix <int>] [-ffn <enum>] [-nsmooth <int>]
DESCRIPTION
gmx dielectric calculates frequency dependent dielectric constants from the
autocorrelation function of the total dipole moment in your simulation. This ACF can be
generated by gmx dipoles. The functional forms of the available functions are:
· One parameter: y = exp(-a_1 x),
· Two parameters: y = a_2 exp(-a_1 x),
· Three parameters: y = a_2 exp(-a_1 x) + (1 - a_2) exp(-a_3 x).
Start values for the fit procedure can be given on the command line. It is also possible
to fix parameters at their start value, use -fix with the number of the parameter you want
to fix.
Three output files are generated, the first contains the ACF, an exponential fit to it
with 1, 2 or 3 parameters, and the numerical derivative of the combination data/fit. The
second file contains the real and imaginary parts of the frequency-dependent dielectric
constant, the last gives a plot known as the Cole-Cole plot, in which the imaginary
component is plotted as a function of the real component. For a pure exponential
relaxation (Debye relaxation) the latter plot should be one half of a circle.
OPTIONS
Options to specify input files:
-f [<.xvg>] (dipcorr.xvg)
xvgr/xmgr file
Options to specify output files:
-d [<.xvg>] (deriv.xvg)
xvgr/xmgr file
-o [<.xvg>] (epsw.xvg)
xvgr/xmgr file
-c [<.xvg>] (cole.xvg)
xvgr/xmgr file
Other options:
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-[no]x1 (yes)
use first column as x-axis rather than first data set
-eint <real> (5)
Time to end the integration of the data and start to use the fit
-bfit <real> (5)
Begin time of fit
-efit <real> (500)
End time of fit
-tail <real> (500)
Length of function including data and tail from fit
-A <real> (0.5)
Start value for fit parameter A
-tau1 <real> (10)
Start value for fit parameter tau1
-tau2 <real> (1)
Start value for fit parameter tau2
-eps0 <real> (80)
epsilon0 of your liquid
-epsRF <real> (78.5)
epsilon of the reaction field used in your simulation. A value of 0 means infinity.
-fix <int> (0)
Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
-ffn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-nsmooth <int> (3)
Number of points for smoothing
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