Provided by: gromacs-data_2023.3-1ubuntu3_all 
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)
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COPYRIGHT
2023, GROMACS development team
2023.3 Oct 19, 2023 GMX-CURRENT(1)