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gmx-dipoles - Compute the total dipole plus fluctuations



gmx-dipoles - Compute the total dipole plus fluctuations


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>]


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.
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 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> (xmgrace)
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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September 15, 2017 2016.4