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GMX-DIELECTRIC(1) GROMACS GMX-DIELECTRIC(1) 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 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 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) Time of first frame to read from trajectory (default unit ps) -e <time> (0) Time of last frame to read from trajectory (default unit ps) -dt <time> (0) Only use frame when t MOD dt = first time (default unit ps) -[no]w (no) View output .xvg, .xpm, .eps and .pdb files -xvg <enum> (xmgrace) 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 SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-DIELECTRIC(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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