1GMX-DIELECTRIC(1)                   GROMACS                  GMX-DIELECTRIC(1)
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NAME

6       gmx-dielectric - Calculate frequency dependent dielectric constants
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SYNOPSIS

9          gmx dielectric [-f [<.xvg>]] [-d [<.xvg>]] [-o [<.xvg>]] [-c [<.xvg>]]
10                       [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
11                       [-xvg <enum>] [-[no]x1] [-eint <real>] [-bfit <real>]
12                       [-efit <real>] [-tail <real>] [-A <real>] [-tau1 <real>]
13                       [-tau2 <real>] [-eps0 <real>] [-epsRF <real>]
14                       [-fix <int>] [-ffn <enum>] [-nsmooth <int>]
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DESCRIPTION

17       gmx dielectric calculates frequency dependent dielectric constants from
18       the autocorrelation function of the total dipole moment in your simula‐
19       tion.  This  ACF can be generated by gmx dipoles.  The functional forms
20       of the available functions are:
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22          · One parameter:    y = exp(-a_1 x),
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24          · Two parameters:   y = a_2 exp(-a_1 x),
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26          · Three parameters: y = a_2 exp(-a_1 x) + (1 - a_2) exp(-a_3 x).
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28       Start values for the fit procedure can be given on  the  command  line.
29       It  is  also  possible to fix parameters at their start value, use -fix
30       with the number of the parameter you want to fix.
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32       Three output files are generated, the first contains the ACF, an  expo‐
33       nential  fit to it with 1, 2 or 3 parameters, and the numerical deriva‐
34       tive of the combination data/fit.  The second file  contains  the  real
35       and imaginary parts of the frequency-dependent dielectric constant, the
36       last gives a plot known as the Cole-Cole plot, in which  the  imaginary
37       component  is  plotted as a function of the real component.  For a pure
38       exponential relaxation (Debye relaxation) the latter plot should be one
39       half of a circle.
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OPTIONS

42       Options to specify input files:
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44       -f [<.xvg>] (dipcorr.xvg)
45              xvgr/xmgr file
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47       Options to specify output files:
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49       -d [<.xvg>] (deriv.xvg)
50              xvgr/xmgr file
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52       -o [<.xvg>] (epsw.xvg)
53              xvgr/xmgr file
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55       -c [<.xvg>] (cole.xvg)
56              xvgr/xmgr file
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58       Other options:
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60       -b <time> (0)
61              Time of first frame to read from trajectory (default unit ps)
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63       -e <time> (0)
64              Time of last frame to read from trajectory (default unit ps)
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66       -dt <time> (0)
67              Only use frame when t MOD dt = first time (default unit ps)
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69       -[no]w (no)
70              View output .xvg, .xpm, .eps and .pdb files
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72       -xvg <enum> (xmgrace)
73              xvg plot formatting: xmgrace, xmgr, none
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75       -[no]x1 (yes)
76              use first column as x-axis rather than first data set
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78       -eint <real> (5)
79              Time to end the integration of the data and start to use the fit
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81       -bfit <real> (5)
82              Begin time of fit
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84       -efit <real> (500)
85              End time of fit
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87       -tail <real> (500)
88              Length of function including data and tail from fit
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90       -A <real> (0.5)
91              Start value for fit parameter A
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93       -tau1 <real> (10)
94              Start value for fit parameter tau1
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96       -tau2 <real> (1)
97              Start value for fit parameter tau2
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99       -eps0 <real> (80)
100              epsilon0 of your liquid
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102       -epsRF <real> (78.5)
103              epsilon  of  the reaction field used in your simulation. A value
104              of 0 means infinity.
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106       -fix <int> (0)
107              Fix parameters at their start values, A (2), tau1 (1),  or  tau2
108              (4)
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110       -ffn <enum> (none)
111              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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113       -nsmooth <int> (3)
114              Number of points for smoothing
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SEE ALSO

117       gmx(1)
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119       More     information    about    GROMACS    is    available    at    <‐
120       http://www.gromacs.org/>.
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123       2019, GROMACS development team
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1282019.2                           Apr 16, 2019                GMX-DIELECTRIC(1)
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