gmx-current(1) GROMACS Manual gmx-current(1)NAMEgmx-current - Calculate dielectric constants and current autocorrela‐
tion 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 func‐
tion, 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. Addition‐
ally, an Einstein-Helfand fit can be used to obtain the static conduc‐
tivity.
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 autocorre‐
lation 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 determina‐
tion of the dielectric constant for system of charged molecules. How‐
ever, 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 ful‐
fill the approximation that the density of the molecules is approxi‐
mately 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 cor‐
responds to infinity (tin-foil boundary conditions).
-bfit <real> (100)
Begin of the fit of the straight line to the MSD of the transla‐
tional 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-current(1)
