1GMX-CURRENT(1)                      GROMACS                     GMX-CURRENT(1)
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NAME

6       gmx-current  -  Calculate dielectric constants and current autocorrela‐
7       tion function
8

SYNOPSIS

10          gmx current [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
11                      [-o [<.xvg>]] [-caf [<.xvg>]] [-dsp [<.xvg>]]
12                      [-md [<.xvg>]] [-mj [<.xvg>]] [-mc [<.xvg>]] [-b <time>]
13                      [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
14                      [-sh <int>] [-[no]nojump] [-eps <real>] [-bfit <real>]
15                      [-efit <real>] [-bvit <real>] [-evit <real>]
16                      [-temp <real>]
17

DESCRIPTION

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

62       Options to specify input files:
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64       -s [<.tpr/.gro/…>] (topol.tpr)
65              Structure+mass(db): tpr gro g96 pdb brk ent
66
67       -n [<.ndx>] (index.ndx) (Optional)
68              Index file
69
70       -f [<.xtc/.trr/…>] (traj.xtc)
71              Trajectory: xtc trr cpt gro g96 pdb tng
72
73       Options to specify output files:
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75       -o [<.xvg>] (current.xvg)
76              xvgr/xmgr file
77
78       -caf [<.xvg>] (caf.xvg) (Optional)
79              xvgr/xmgr file
80
81       -dsp [<.xvg>] (dsp.xvg)
82              xvgr/xmgr file
83
84       -md [<.xvg>] (md.xvg)
85              xvgr/xmgr file
86
87       -mj [<.xvg>] (mj.xvg)
88              xvgr/xmgr file
89
90       -mc [<.xvg>] (mc.xvg) (Optional)
91              xvgr/xmgr file
92
93       Other options:
94
95       -b <time> (0)
96              Time of first frame to read from trajectory (default unit ps)
97
98       -e <time> (0)
99              Time of last frame to read from trajectory (default unit ps)
100
101       -dt <time> (0)
102              Only use frame when t MOD dt = first time (default unit ps)
103
104       -[no]w (no)
105              View output .xvg, .xpm, .eps and .pdb files
106
107       -xvg <enum> (xmgrace)
108              xvg plot formatting: xmgrace, xmgr, none
109
110       -sh <int> (1000)
111              Shift of the frames for averaging the correlation functions  and
112              the mean-square displacement.
113
114       -[no]nojump (yes)
115              Removes jumps of atoms across the box.
116
117       -eps <real> (0)
118              Dielectric  constant  of  the surrounding medium. The value zero
119              corresponds to infinity (tin-foil boundary conditions).
120
121       -bfit <real> (100)
122              Begin of the fit of the straight line to the MSD of the transla‐
123              tional fraction of the dipole moment.
124
125       -efit <real> (400)
126              End  of  the fit of the straight line to the MSD of the transla‐
127              tional fraction of the dipole moment.
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129       -bvit <real> (0.5)
130              Begin of the fit of  the  current  autocorrelation  function  to
131              a*t^b.
132
133       -evit <real> (5)
134              End of the fit of the current autocorrelation function to a*t^b.
135
136       -temp <real> (300)
137              Temperature for calculating epsilon.
138

SEE ALSO

140       gmx(1)
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142       More     information    about    GROMACS    is    available    at    <‐
143       http://www.gromacs.org/>.
144
146       2019, GROMACS development team
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1512018.7                           May 29, 2019                   GMX-CURRENT(1)
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