- buster 2019.1-1
- testing 2019.3-2
- unstable 2019.4-1
- experimental 2020~beta1-2

GMX-CURRENT(1) | GROMACS | GMX-CURRENT(1) |

# 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>] [-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)- Time of first frame to read from trajectory (default unit ps)
**-e**<time> (0)- Time of last frame to read from trajectory (default unit ps)
**-dt**<time> (0)- Only use frame when t MOD dt = first time (default unit 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 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.
**-temp**<real> (300)- Temperature for calculating epsilon.

# SEE ALSO¶

**gmx(1)**

More information about GROMACS is available at
<*http://www.gromacs.org/*>.

# COPYRIGHT¶

2019, GROMACS development teamFebruary 15, 2019 | 2019.1 |