g_dipoles(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dipoles(1)
g_dipoles - computes the total dipole plus fluctuations
g_dipoles -en ener.edr -f traj.xtc -s topol.tpr -n index.ndx -o Mtot.xvg -eps epsilon.xvg -a aver.xvg -d dipdist.xvg -c dipcorr.xvg -g
gkr.xvg -adip adip.xvg -dip3d dip3d.xvg -cos cosaver.xvg -cmap cmap.xpm -q quadrupole.xvg -slab slab.xvg -[no]h -[no]version -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 -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
-ncskip int -beginfit real -endfit real
g_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 con-
tains |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 com-
puted 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
g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft
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.
-en ener.edr Input, Opt.
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input, Opt.
-o Mtot.xvg Output
-eps epsilon.xvg Output
-a aver.xvg Output
-d dipdist.xvg Output
-c dipcorr.xvg Output, Opt.
-g gkr.xvg Output, Opt.
-adip adip.xvg Output, Opt.
-dip3d dip3d.xvg Output, Opt.
-cos cosaver.xvg Output, Opt.
-cmap cmap.xpm Output, Opt.
X PixMap compatible matrix file
-q quadrupole.xvg Output, Opt.
-slab slab.xvg Output, Opt.
Print help info and quit
Print version info and quit
-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)
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-mu real -1
dipole of a single molecule (in Debye)
-mumax real 5
max dipole in Debye (for histrogram)
-epsilonRF real 0
epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity
-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 or total
Calculate |cos theta| between all pairs of molecules. May be slow
-ncos int 1
Must be 1 or 2. Determines whether the cos is computed between all molecules in one group, or between molecules in two different groups.
This turns on the -gkr flag.
-axis string Z
Take the normal on the computational box in direction X, Y or Z.
-sl int 10
Divide the box in nr 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
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
-P enum 0
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
-fitfn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-ncskip int 0
Skip N points in the output file of correlation functions
-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
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_dipoles(1)