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 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 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/>.