share/html/online/g_dipoles.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_dipoles</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_dipoles</tt> computes the total dipole plus fluctuations of a simulation
  18 system. From this you can compute e.g. the dielectric constant for
  19 low-dielectric media.
  20 For molecules with a net charge, the net charge is subtracted at
  21 center of mass of the molecule.<p>
  22 The file <tt>Mtot.<a href="xvg.html">xvg</a></tt> contains the total dipole moment of a frame, the
  23 components as well as the norm of the vector.
  24 The file <tt>aver.<a href="xvg.html">xvg</a></tt> contains <|&mu;|^2> and |<&mu;>|^2 during the
  25 simulation.
  26 The file <tt>dipdist.<a href="xvg.html">xvg</a></tt> contains the distribution of dipole moments during
  27 the simulation
  28 The value of <tt>-mumax</tt> is used as the highest value in the distribution graph.<p>
  29 Furthermore, the dipole autocorrelation function will be computed when
  30 option <tt>-corr</tt> is used. The output file name is given with the <tt>-c</tt>
  31 option.
  32 The correlation functions can be averaged over all molecules
  33 (<tt>mol</tt>), plotted per molecule separately (<tt>molsep</tt>)
  34 or it can be computed over the total dipole moment of the simulation box
  35 (<tt>total</tt>).<p>
  36 Option <tt>-g</tt> produces a plot of the distance dependent Kirkwood
  37 G-factor, as well as the average cosine of the angle between the dipoles
  38 as a function of the distance. The plot also includes gOO and hOO
  39 according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the same plot,
  40 we also include the energy per scale computed by taking the inner product of
  41 the dipoles divided by the distance to the third power.<p>
  42 <p>
  43 EXAMPLES<p>
  44 <tt>g_dipoles -corr mol -P 1 -o dip_sqr -mu 2.273 -mumax 5.0</tt><p>
  45 This will calculate the autocorrelation function of the molecular
  46 dipoles using a first order Legendre polynomial of the angle of the
  47 dipole vector and itself a time t later. For this calculation 1001
  48 frames will be used. Further, the dielectric constant will be calculated
  49 using an <tt>-epsilonRF</tt> of infinity (default), temperature of 300 K (default) and
  50 an average dipole moment of the molecule of 2.273 (SPC). For the
  51 distribution function a maximum of 5.0 will be used.
  52 <P>
  53 <H3>Files</H3>
  54 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  55 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-en</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    Mtot.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> epsilon.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    aver.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipdist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipcorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     gkr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-adip</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    adip.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-dip3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   dip3d.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-cos</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> cosaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-cmap</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    cmap.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">quadrupole.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-slab</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    slab.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  72 </TABLE>
  73 <P>
  74 <H3>Other options</H3>
  75 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  76 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-mu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> dipole of a single molecule (in Debye) </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> max dipole in Debye (for histogram) </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> &epsilon; of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip steps in the output (but not in the computations) </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300   </tt> </TD><TD> Average temperature of the simulation (needed for dielectric constant calculation) </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Correlation function to calculate: <tt>none</tt>, <tt>mol</tt>, <tt>molsep</tt> or <tt>total</tt> </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Calculate |cos(&theta;)| between all pairs of molecules. May be slow </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-ncos</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Must be 1 or 2. Determines whether the <cos(&theta;)> is computed between all molecules in one group, or between molecules in two different groups. This turns on the <tt>-g</tt> flag. </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-axis</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the computational box in direction X, Y or Z. </TD></TD>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box into this number of slices. </TD></TD>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-gkratom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> 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 </TD></TD>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-gkratom2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules </TD></TD>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-rcmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used. </TD></TD>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the <tt>.<a href="xpm.html">xpm</a></tt> file from the <tt>-cmap</tt> option. By default the cosine of the angle between the dipoles is plotted. </TD></TD>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of colors in the cmap output </TD></TD>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-ndegrees</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>90</tt> </TD><TD> Number of divisions on the <it>y</it>-axis in the cmap output (for 180 degrees) </TD></TD>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Normalize ACF </TD></TD>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
 108 </TABLE>
 109 <P>
 110 <hr>
 111 <div ALIGN=RIGHT>
 112 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 113 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 114 </div>
 115 </BODY>