DragonFly On-Line Manual Pages

gmx-current(1)                  GROMACS Manual                  gmx-current(1)

NAME
       gmx-current - Calculate dielectric constants and current
       autocorrelation function

SYNOPSIS
       gmx current [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                   [-f [<.xtc/.trr/...>]] [-o [<.xvg>]] [-caf [<.xvg>]]
                   [-dsp [<.xvg>]] [-md [<.xvg>]] [-mj [<.xvg>]]
                   [-mc [<.xvg>]] [-nice <int>] [-b <time>] [-e <time>]
                   [-dt <time>] [-[no]w] [-xvg <enum>] [-sh <int>]
                   [-[no]nojump] [-eps <real>] [-bfit <real>] [-efit <real>]
                   [-bvit <real>] [-evit <real>] [-tr <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 and output files:

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

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

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

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

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

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

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

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

       -mc [<.xvg>] (mc.xvg) (Output, Optional)
           xvgr/xmgr file

       Other options:

       -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]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*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/>.

VERSION 5.0.6                                                   gmx-current(1)