g_dipoles(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dipoles(1)
NAME
g_dipoles - computes the total dipole plus fluctuations
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
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
DESCRIPTION
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
power.
EXAMPLES
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.
FILES
-en ener.edr Input, Opt.
Energy file
-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.
Index file
-o Mtot.xvg Output
xvgr/xmgr file
-eps epsilon.xvg Output
xvgr/xmgr file
-a aver.xvg Output
xvgr/xmgr file
-d dipdist.xvg Output
xvgr/xmgr file
-c dipcorr.xvg Output, Opt.
xvgr/xmgr file
-g gkr.xvg Output, Opt.
xvgr/xmgr file
-adip adip.xvg Output, Opt.
xvgr/xmgr file
-dip3d dip3d.xvg Output, Opt.
xvgr/xmgr file
-cos cosaver.xvg Output, Opt.
xvgr/xmgr file
-cmap cmap.xpm Output, Opt.
X PixMap compatible matrix file
-q quadrupole.xvg Output, Opt.
xvgr/xmgr file
-slab slab.xvg Output, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
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)
-[no]wno
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
(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 or total
-[no]pairsyes
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
used.
-[no]phino
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]normalizeyes
Normalize ACF
-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
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_dipoles(1)