This is the command gmx-dipoles 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-dipoles - Compute the total dipole plus fluctuations
SYNOPSIS
gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-eps [<.xvg>]] [-a [<.xvg>]]
[-d [<.xvg>]] [-c [<.xvg>]] [-g [<.xvg>]]
[-adip [<.xvg>]] [-dip3d [<.xvg>]] [-cos [<.xvg>]]
[-cmap [<.xpm>]] [-slab [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-mu <real>]
[-mumax <real>] [-epsilonRF <real>] [-skip <int>]
[-temp <real>] [-corr <enum>] [-[no]pairs] [-[no]quad]
[-ncos <int>] [-axis <string>] [-sl <int>]
[-gkratom <int>] [-gkratom2 <int>] [-rcmax <real>]
[-[no]phi] [-nlevels <int>] [-ndegrees <int>]
[-acflen <int>] [-[no]normalize] [-P <enum>]
[-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
DESCRIPTION
gmx dipoles computes the total dipole plus fluctuations of a simulation system. From this
you can compute e.g. the dielectric constant for low-dielectric media. For molecules with
a net charge, the net charge is subtracted at center of mass of the molecule.
The file Mtot.xvg contains the total dipole moment of a frame, the components as well as
the norm of the vector. The file aver.xvg contains <|mu|^2> and |<mu>|^2 during the
simulation. The file dipdist.xvg contains the distribution of dipole moments during the
simulation The value of -mumax is used as the highest value in the distribution graph.
Furthermore, the dipole autocorrelation function will be computed when option -corr is
used. The output file name is given with the -c option. The correlation functions can be
averaged over all molecules (mol), plotted per molecule separately (molsep) or it can be
computed over the total dipole moment of the simulation box (total).
Option -g produces a plot of the distance dependent Kirkwood G-factor, as well as the
average cosine of the angle between the dipoles as a function of the distance. The plot
also includes gOO and hOO according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp
6386-6395. In the same plot, we also include the energy per scale computed by taking the
inner product of the dipoles divided by the distance to the third power.
EXAMPLES
gmx dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0
This will calculate the autocorrelation function of the molecular dipoles using a first
order Legendre polynomial of the angle of the dipole vector and itself a time t later. For
this calculation 1001 frames will be used. Further, the dielectric constant will be
calculated using an -epsilonRF of infinity (default), temperature of 300 K (default) and
an average dipole moment of the molecule of 2.273 (SPC). For the distribution function a
maximum of 5.0 will be used.
OPTIONS
Options to specify input files:
-en [<.edr>] (ener.edr) (Optional)
Energy file
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to specify output files:
-o [<.xvg>] (Mtot.xvg)
xvgr/xmgr file
-eps [<.xvg>] (epsilon.xvg)
xvgr/xmgr file
-a [<.xvg>] (aver.xvg)
xvgr/xmgr file
-d [<.xvg>] (dipdist.xvg)
xvgr/xmgr file
-c [<.xvg>] (dipcorr.xvg) (Optional)
xvgr/xmgr file
-g [<.xvg>] (gkr.xvg) (Optional)
xvgr/xmgr file
-adip [<.xvg>] (adip.xvg) (Optional)
xvgr/xmgr file
-dip3d [<.xvg>] (dip3d.xvg) (Optional)
xvgr/xmgr file
-cos [<.xvg>] (cosaver.xvg) (Optional)
xvgr/xmgr file
-cmap [<.xpm>] (cmap.xpm) (Optional)
X PixMap compatible matrix file
-slab [<.xvg>] (slab.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
-mu <real> (-1)
dipole of a single molecule (in Debye)
-mumax <real> (5)
max dipole in Debye (for histogram)
-epsilonRF <real> (0)
epsilon of the reaction field used during the simulation, needed for dielectric
constant calculation. WARNING: 0.0 means infinity (default)
-skip <int> (0)
Skip steps in the output (but not in the computations)
-temp <real> (300)
Average temperature of the simulation (needed for dielectric constant calculation)
-corr <enum> (none)
Correlation function to calculate: none, mol, molsep, total
-[no]pairs (yes)
Calculate |cos(theta)| between all pairs of molecules. May be slow
-[no]quad (no)
Take quadrupole into account
-ncos <int> (1)
Must be 1 or 2. Determines whether the <cos(theta)> is computed between all
molecules in one group, or between molecules in two different groups. This turns on
the -g flag.
-axis <string> (Z)
Take the normal on the computational box in direction X, Y or Z.
-sl <int> (10)
Divide the box into this number of slices.
-gkratom <int> (0)
Use the n-th atom of a molecule (starting from 1) to calculate the distance between
molecules rather than the center of charge (when 0) in the calculation of distance
dependent Kirkwood factors
-gkratom2 <int> (0)
Same as previous option in case ncos = 2, i.e. dipole interaction between two
groups of molecules
-rcmax <real> (0)
Maximum distance to use in the dipole orientation distribution (with ncos == 2). If
zero, a criterion based on the box length will be used.
-[no]phi (no)
Plot the 'torsion angle' defined as the rotation of the two dipole vectors around
the distance vector between the two molecules in the .xpm file from the -cmap
option. By default the cosine of the angle between the dipoles is plotted.
-nlevels <int> (20)
Number of colors in the cmap output
-ndegrees <int> (90)
Number of divisions on the y-axis in the cmap output (for 180 degrees)
-acflen <int> (-1)
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-beginfit <real> (0)
Time where to begin the exponential fit of the correlation function
-endfit <real> (-1)
Time where to end the exponential fit of the correlation function, -1 is until the
end
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