NAME¶
g_current - calculate current autocorrelation function of system
VERSION 4.5.4-dev-20110404-bc5695c
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. eps=0.0 corresponds to
eps=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/>.