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g_dielectric_d

NAME

g_dielectric - calculates frequency dependent dielectric constants

SYNOPSIS

g_dielectric -f Mtot.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[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

dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your simulation. This ACF can be generated by g_dipoles. For an estimate of the error you can run g_statistics on the ACF, and use the output thus generated for this program. The functional forms of the available functions are:

One parmeter : y = Exp[-a1 x] Two parmeters : y = a2 Exp[-a1 x] Three parmeter: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x] Startvalues for the fit procedure can be given on the commandline. 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

FILES

-f Mtot.xvg Input
 xvgr/xmgr file 

-d deriv.xvg Output
 xvgr/xmgr file 

-o epsw.xvg Output
 xvgr/xmgr file 

-c cole.xvg Output
 xvgr/xmgr file 

OTHER OPTIONS

-[no]h no
 Print help info and quit

-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

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[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 were 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
 Epsilon 0 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 or exp9

-nsmooth int 3
 Number of points for smoothing

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.