g_dipoles (1) - Linux Manuals

g_dipoles: computes the total dipole plus fluctuations


g_dipoles - computes the total dipole plus fluctuations



g_dipoles -enx 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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -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


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 mu_max 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 seperately ( 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, 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.


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.


-enx ener.edr Input, Opt.
 Energy file: edr ene 

-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 


 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)

 View output xvg, xpm, eps and pdb files

 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)

-corr enum none
 Correlation function to calculate:  none mol molsep or  total

 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 mole cules 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 criterium 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.

-nlevels int 20
 Number of colors in the cmap output

-ndegrees int 90
 Number of divisions on the y-axis in the camp output (for 180 degrees)

-acflen int -1
 Length of the ACF, default is half the number of frames

 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



More information about GROMACS is available at <http://www.gromacs.org/>.