g_current(1)

1g_current(1)              GROMACS suite, VERSION 4.5              g_current(1)
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NAME

6       g_current - calculate current autocorrelation function of system
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8       VERSION 4.5
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SYNOPSIS

11       g_current  -s  topol.tpr  -n  index.ndx -f traj.xtc -o current.xvg -caf
12       caf.xvg -dsp dsp.xvg -md md.xvg -mj mj.xvg -mc mc.xvg -[no]h  -[no]ver‐
13       sion  -nice  int  -b  time  -e  time  -dt time -[no]w -xvg enum -sh int
14       -[no]nojump -eps real -bfit real -efit real -bvit real -evit  real  -tr
15       real -temp real
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DESCRIPTION

18       This  is  a  tool for calculating the current autocorrelation function,
19       the correlation of the rotational and translational  dipole  moment  of
20       the  system,  and the resulting static dielectric constant. To obtain a
21       reasonable result the index group has to be neutral.   Furthermore  the
22       routine  is capable of extracting the static conductivity from the cur‐
23       rent autocorrelation function, if velocities are given. Additionally an
24       Einstein-Helfand fit also allows to get the static conductivity.
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27       The  flag   -caf is for the output of the current autocorrelation func‐
28       tion and  -mc writes the correlation of  the  rotational  and  transla‐
29       tional  part  of  the  dipole moment in the corresponding file. However
30       this option is only available for trajectories  containing  velocities.
31       Options  -sh and  -tr are responsible for the averaging and integration
32       of the autocorrelation functions. Since averaging proceeds by  shifting
33       the  starting  point  through the trajectory, the shift can be modified
34       with  -sh to enable the choice of uncorrelated starting points. Towards
35       the  end,  statistical inaccuracy grows and integrating the correlation
36       function only yields reliable values until a certain  point,  depending
37       on  the  number  of  frames. The option  -tr controls the region of the
38       integral taken into account for calculating the static dielectric  con‐
39       stant.
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42       Option   -temp sets the temperature required for the computation of the
43       static dielectric constant.
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46       Option  -eps controls the dielectric constant of the surrounding medium
47       for  simulations  using  a  Reaction Field or dipole corrections of the
48       Ewald summation (eps=0 corresponds to tin-foil boundary conditions).
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51        -[no]nojump unfolds the coordinates to allow free diffusion.  This  is
52       required  to get a continuous translational dipole moment, required for
53       the Einstein-Helfand fit. The resuls from the fit  allow  to  determine
54       the  dielectric constant for system of charged molecules. However it is
55       also possible to extract the dielectric constant from the  fluctuations
56       of  the total dipole moment in folded coordinates. But this options has
57       to be used with care, since only very  short  time  spans  fulfill  the
58       approximation,  that the density of the molecules is approximately con‐
59       stant and the averages are already converged. To be on the  safe  side,
60       the  dielectric constant should be calculated with the help of the Ein‐
61       stein-Helfand method for the translational part of the dielectric  con‐
62       stant.
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FILES

65       -s topol.tpr Input
66        Structure+mass(db): tpr tpb tpa gro g96 pdb
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68       -n index.ndx Input, Opt.
69        Index file
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71       -f traj.xtc Input
72        Trajectory: xtc trr trj gro g96 pdb cpt
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74       -o current.xvg Output
75        xvgr/xmgr file
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77       -caf caf.xvg Output, Opt.
78        xvgr/xmgr file
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80       -dsp dsp.xvg Output
81        xvgr/xmgr file
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83       -md md.xvg Output
84        xvgr/xmgr file
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86       -mj mj.xvg Output
87        xvgr/xmgr file
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89       -mc mc.xvg Output, Opt.
90        xvgr/xmgr file
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OTHER OPTIONS

94       -[no]hno
95        Print help info and quit
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97       -[no]versionno
98        Print version info and quit
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100       -nice int 0
101        Set the nicelevel
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103       -b time 0
104        First frame (ps) to read from trajectory
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106       -e time 0
107        Last frame (ps) to read from trajectory
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109       -dt time 0
110        Only use frame when t MOD dt = first time (ps)
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112       -[no]wno
113        View output xvg, xpm, eps and pdb files
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115       -xvg enum xmgrace
116        xvg plot formatting:  xmgrace,  xmgr or  none
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118       -sh int 1000
119        Shift  of  the  frames for averaging the correlation functions and the
120       mean-square displacement.
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122       -[no]nojumpyes
123        Removes jumps of atoms across the box.
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125       -eps real 0
126        Dielectric constant of the surrounding medium. eps=0.0 corresponds  to
127       eps=infinity (thinfoil boundary conditions).
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129       -bfit real 100
130        Begin  of the fit of the straight line to the MSD of the translational
131       fraction of the dipole moment.
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133       -efit real 400
134        End of the fit of the straight line to the MSD  of  the  translational
135       fraction of the dipole moment.
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137       -bvit real 0.5
138        Begin of the fit of the current autocorrelation function to a*tb.
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140       -evit real 5
141        End of the fit of the current autocorrelation function to a*tb.
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143       -tr real 0.25
144        Fraction of the trajectory taken into account for the integral.
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146       -temp real 300
147        Temperature for calculating epsilon.
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO