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

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 mu_max is used as the highest value in the distribution graph.

Furthermore the dipole autocorrelation function will be computed, when option -c is used. It can be averaged over all molecules, or (with option -avercorr) it can be computed as the autocorrelation of the total dipole moment of the simulation box.

At the moment the dielectric constant is calculated only correct if a rectangular or cubic simulation box is used.

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, JCP 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 -P1 -n mols -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

-enx ener.edr Input, Opt.

Generic energy: edr ene

-f traj.xtc Input

Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input

Generic run input: tpr tpb tpa xml

-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

-q quadrupole.xvg Output, Opt.

xvgr/xmgr file

-slab slab.xvg Output, Opt.

xvgr/xmgr file

OTHER OPTIONS

-[no]h no

Print help 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]w no

View output xvg, xpm, eps and pdb files

-[no]xvgr yes

Add specific codes (legends etc.) in the output xvg files for the

xmgrace program

-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

dieclectric 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)

-[no]avercorr no

calculate AC function of average dipole moment of the simulation box

rather than average of AC function per molecule

-[no]pairs yes

Calculate |cos theta| between all pairs of molecules. May be slow

-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

-acflen int -1

Length of the ACF, default is half the number of frames

-[no]normalize yes

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 or exp9

-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 till the end

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.

Mon 29 Aug 2005 g_dipoles(1)