g_dipoles(1) - Linux man page

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 -adipadip.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 -correnum -[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