gmx-dielectric(1) GROMACS Manual gmx-dielectric(1)NAMEgmx-dielectric - Calculate frequency dependent dielectric constants
SYNOPSIS
gmx dielectric [-f [<.xvg>]] [-d [<.xvg>]] [-o [<.xvg>]]
[-c [<.xvg>]] [-nice <int>] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-[no]fft] [-[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 simula‐
tion. 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 expo‐
nential fit to it with 1, 2 or 3 parameters, and the numerical deriva‐
tive 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 and output files:
-f [<.xvg>] (dipcorr.xvg) (Input)
xvgr/xmgr file
-d [<.xvg>] (deriv.xvg) (Output)
xvgr/xmgr file
-o [<.xvg>] (epsw.xvg) (Output)
xvgr/xmgr file
-c [<.xvg>] (cole.xvg) (Output)
xvgr/xmgr file
Other options:
-nice <int> (19)
Set the nicelevel
-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> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]fft (no)
use fast fourier transform for correlation function
-[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, vac, exp5, exp7, exp9, erf‐
fit
-nsmooth <int> (3)
Number of points for smoothing
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-dielectric(1)
