table of contents
g_dipoles(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_dipoles(1) |
NAME¶
g_dipoles - computes the total dipole plus fluctuationsSYNOPSIS¶
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 realDESCRIPTION¶
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.FILES¶
-en ener.edr Input, Opt.Energy file
Trajectory: xtc trr trj gro g96 pdb cpt
Run input file: tpr tpb tpa
Index file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
X PixMap compatible matrix file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
dipole of a single molecule (in Debye)
max dipole in Debye (for histrogram)
epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)
Skip steps in the output (but not in the computations)
Average temperature of the simulation (needed for dielectric constant calculation)
Correlation function to calculate: none, mol, molsep or total
Calculate |cos theta| between all pairs of molecules. May be slow
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.
Take the normal on the computational box in direction X, Y or Z.
Divide the box in nr slices.
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
Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules
Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used.
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.
Number of colors in the cmap output
Number of divisions on the y-axis in the cmap output (for 180 degrees)
Length of the ACF, default is half the number of frames
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
Skip N points in the output file of correlation functions
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |