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NAME

       g_current - calculates dielectric constants for charged systems

       VERSION 4.0.1

SYNOPSIS

       g_current  -s  topol.tpr  -n  index.ndx -f traj.xtc -o current.xvg -caf
       caf.xvg -dsp dsp.xvg -md md.xvg -mj mj.xvg -mc mc.xvg -[no]h -nice  int
       -b time -e time -dt time -[no]w -[no]xvgr -sh int -[no]nojump -eps real
       -bfit real -efit real -bvit real -evit real -tr real -temp real

DESCRIPTION

       This 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 also allows to get 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 resuls from the fit allow to determine
       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 options  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.

FILES

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -o current.xvg Output
        xvgr/xmgr file

       -caf caf.xvg Output, Opt.
        xvgr/xmgr file

       -dsp dsp.xvg Output
        xvgr/xmgr file

       -md md.xvg Output
        xvgr/xmgr file

       -mj mj.xvg Output
        xvgr/xmgr file

       -mc mc.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -nice int 0
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

       -[no]wno
        View output xvg, xpm, eps and pdb files

       -[no]xvgryes
        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

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

       -[no]nojumpyes
        Removes jumps of atoms across the box.

       -eps real 0
        Dielectric constant of the surrounding medium. eps=0.0 corresponds  to
       eps=infinity (thinfoil 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*tb.

       -evit real 5
        End of the fit of the current autocorrelation function to a*tb.

       -tr real 0.25
        Fraction of the trajectory taken into account for the integral.

       -temp real 300
        Temperature for calculating epsilon.

SEE ALSO

       gromacs(7)

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

                                Thu 16 Oct 2008                   g_current(1)