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NAME

       gmx-current - Calculate dielectric constants and current autocorrelation function

SYNOPSIS

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

DESCRIPTION

       gmx  current  is  a  tool  for  calculating  the  current  autocorrelation  function,  the
       correlation of the rotational and translational dipole  moment  of  the  system,  and  the
       resulting  static  dielectric constant. To obtain a reasonable result, the index group has
       to be neutral.  Furthermore, the routine is capable of extracting the static  conductivity
       from  the  current  autocorrelation  function,  if  velocities are given. Additionally, an
       Einstein-Helfand fit can be used to obtain the static conductivity.

       The flag -caf is for the output of the current autocorrelation function and -mc writes the
       correlation  of  the  rotational  and  translational  part  of  the  dipole  moment in the
       corresponding file. However, this option is only  available  for  trajectories  containing
       velocities.   Options -sh and -tr are responsible for the averaging and integration of the
       autocorrelation functions. Since averaging proceeds by shifting the starting point through
       the  trajectory,  the  shift can be modified with -sh to enable the choice of uncorrelated
       starting points. Towards  the  end,  statistical  inaccuracy  grows  and  integrating  the
       correlation  function  only yields reliable values until a certain point, depending on the
       number of frames. The option -tr controls the region of the integral  taken  into  account
       for calculating the static dielectric constant.

       Option  -temp  sets  the temperature required for the computation of the static dielectric
       constant.

       Option -eps controls the dielectric constant of the  surrounding  medium  for  simulations
       using a Reaction Field or dipole corrections of the Ewald summation (-eps=0 corresponds to
       tin-foil boundary conditions).

       -[no]nojump unfolds the coordinates to allow free diffusion. This is  required  to  get  a
       continuous translational dipole moment, required for the Einstein-Helfand fit. The results
       from the fit allow the determination of the dielectric  constant  for  system  of  charged
       molecules.  However,  it  is  also  possible  to  extract the dielectric constant from the
       fluctuations of the total dipole moment in folded coordinates. But this option has  to  be
       used  with  care,  since  only  very  short  time spans fulfill the approximation that the
       density of the molecules is approximately constant and the averages are already converged.
       To  be on the safe side, the dielectric constant should be calculated with the help of the
       Einstein-Helfand method for the translational part of the dielectric constant.

OPTIONS

       Options to specify input files:

       -s [<.tpr/.gro/…>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       Options to specify output files:

       -o [<.xvg>] (current.xvg)
              xvgr/xmgr file

       -caf [<.xvg>] (caf.xvg) (Optional)
              xvgr/xmgr file

       -dsp [<.xvg>] (dsp.xvg)
              xvgr/xmgr file

       -md [<.xvg>] (md.xvg)
              xvgr/xmgr file

       -mj [<.xvg>] (mj.xvg)
              xvgr/xmgr file

       -mc [<.xvg>] (mc.xvg) (Optional)
              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

       -sh <int> (1000)
              Shift of the frames for averaging the correlation  functions  and  the  mean-square
              displacement.

       -[no]nojump (yes)
              Removes jumps of atoms across the box.

       -eps <real> (0)
              Dielectric  constant  of  the  surrounding  medium.  The  value zero corresponds to
              infinity (tin-foil boundary conditions).

       -bfit <real> (100)
              Begin of the fit of the straight line to the MSD of the translational  fraction  of
              the dipole moment.

       -efit <real> (400)
              End of the fit of the straight line to the MSD of the translational fraction of the
              dipole moment.

       -bvit <real> (0.5)
              Begin of the fit of the current autocorrelation function to a*t^b.

       -evit <real> (5)
              End of the fit of the current autocorrelation function to a*t^b.

       -temp <real> (300)
              Temperature for calculating epsilon.

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team