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)