This is the command gmx-current that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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>] [-tr <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)
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>
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.
-tr <real> (0.25)
Fraction of the trajectory taken into account for the integral.
-temp <real> (300)
Temperature for calculating epsilon.
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