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g_dipolesMain Table of Contents |
VERSION 3.2.0
Sun 25 Jan 2004
| VERSION 3.2.0 |
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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| -q | quadrupole.xvg | Output, Opt. | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -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 | bool | no | calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule |
| -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 | bool | 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 |