g_dielectric (1) - Linux Manuals

g_dielectric: calculates frequency dependent dielectric constants


g_dielectric - calculates frequency dependent dielectric constants



g_dielectric -f dipcorr.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


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


-f dipcorr.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 


 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

 use fast fourier transform for correlation function

 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



More information about GROMACS is available at <http://www.gromacs.org/>.