Provided by: gromacs-data_4.6.5-1build1_all 
NAME
g_current - calculate current autocorrelation function of system
VERSION 4.6.5
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 -[no]version -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
g_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.
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
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-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. 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/>.
Mon 2 Dec 2013 g_current(1)