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g_dielectric(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dielectric(1) NAME
g_dielectric - calculates frequency dependent dielectric constants VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_dielectric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg -[no]h -[no]version -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
g_dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your sim- ulation. 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 parameter: y = Exp[-a1 x], Two parameters: y = a2 Exp[-a1 x], Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 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 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. FILES
-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 OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version 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]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]fftno use fast fourier transform for correlation function -[no]x1yes 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 or erffit -nsmooth int 3 Number of points for smoothing SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_dielectric(1)
