NAME¶

gmx-dipoles - Compute the total dipole plus fluctuations

SYNOPSIS¶

gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]]
[-s [<.tpr/.tpb/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
[-eps [<.xvg>]] [-a [<.xvg>]] [-d [<.xvg>]] [-c [<.xvg>]]
[-g [<.xvg>]] [-adip [<.xvg>]] [-dip3d [<.xvg>]]
[-cos [<.xvg>]] [-cmap [<.xpm>]] [-slab [<.xvg>]]
[-nice <int>] [-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 and output files: -en [<.edr>] (ener.edr) (Input, Optional)
Energy file -f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa -n [<.ndx>] (index.ndx) (Input, Optional)
Index file -o [<.xvg>] (Mtot.xvg) (Output)
xvgr/xmgr file -eps [<.xvg>] (epsilon.xvg) (Output)
xvgr/xmgr file -a [<.xvg>] (aver.xvg) (Output)
xvgr/xmgr file -d [<.xvg>] (dipdist.xvg) (Output)
xvgr/xmgr file -c [<.xvg>] (dipcorr.xvg) (Output, Optional)
xvgr/xmgr file -g [<.xvg>] (gkr.xvg) (Output, Optional)
xvgr/xmgr file -adip [<.xvg>] (adip.xvg) (Output, Optional)
xvgr/xmgr file -dip3d [<.xvg>] (dip3d.xvg) (Output, Optional)
xvgr/xmgr file -cos [<.xvg>] (cosaver.xvg) (Output, Optional)
xvgr/xmgr file -cmap [<.xpm>] (cmap.xpm) (Output, Optional)
X PixMap compatible matrix file -slab [<.xvg>] (slab.xvg) (Output, Optional)
xvgr/xmgr file Other options: -nice <int> (19)
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 -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, vac, exp5, exp7, exp9, erffit -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

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.