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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_densmap</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 4.0<br>
  13 Sun 18 Jan 2009</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_densmap computes 2D number-density maps.
  18 It can make planar and axial-radial density maps.
  19 The output <tt>.<a href="xpm.html">xpm</a></tt> file can be visualized with for instance xv
  20 and can be converted to postscript with <a href="xpm2ps.html">xpm2ps</a>.
  21 <p>
  22 The default analysis is a 2-D number-density <a href="map.html">map</a> for a selected
  23 group of atoms in the x-y plane.
  24 The averaging direction can be changed with the option <tt>-aver</tt>.
  25 When <tt>-xmin</tt> and/or <tt>-xmax</tt> are set only atoms that are
  26 within the limit(s) in the averaging direction are taken into account.
  27 The grid spacing is set with the option <tt>-bin</tt>.
  28 When <tt>-n1</tt> or <tt>-n2</tt> is non-zero, the grid
  29 size is set by this option.
  30 Box size fluctuations are properly taken into account.
  31 <p>
  32 When options <tt>-amax</tt> and <tt>-rmax</tt> are set, an axial-radial
  33 number-density <a href="map.html">map</a> is made. Three groups should be supplied, the centers
  34 of mass of the first two groups define the axis, the third defines the
  35 analysis group. The axial direction goes from -amax to +amax, where
  36 the center is defined as the midpoint between the centers of mass and
  37 the positive direction goes from the first to the second center of mass.
  38 The radial direction goes from 0 to rmax or from -rmax to +rmax
  39 when the <tt>-mirror</tt> option has been set.
  40 <p>
  41 The normalization of the output is set with the <tt>-unit</tt> option.
  42 The default produces a true number density. Unit <tt>nm-2</tt> leaves out
  43 the normalization for the averaging or the angular direction.
  44 Option <tt>count</tt> produces the count for each grid cell.
  45 When you do not want the scale in the output to go
  46 from zero to the maximum density, you can set the maximum
  47 with the option <tt>-dmax</tt>.
  48 <P>
  49 <H3>Files</H3>
  50 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  51 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  52 <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>
  53 <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, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  54 <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>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> densmap.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  56 </TABLE>
  57 <P>
  58 <H3>Other options</H3>
  59 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  60 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  61 <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>
  62 <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>
  63 <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>
  64 <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>
  65 <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>
  66 <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 <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02  </tt> </TD><TD> Grid size (nm) </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-aver</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> The direction to average over: <tt>z</tt>, <tt>y</tt> or <tt>x</tt> </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-xmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Minimum coordinate for averaging </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-xmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Maximum coordinate for averaging </TD></TD>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-n1</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in the first direction </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in the second direction </TD></TD>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-amax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum axial distance from the center </TD></TD>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum radial distance </TD></TD>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mirror</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Add the mirror image below the axial axis </TD></TD>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-unit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>nm-3</tt> </TD><TD> Unit for the output: <tt>nm-3</tt>, <tt>nm-2</tt> or <tt>count</tt> </TD></TD>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-dmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Minimum density in output </TD></TD>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-dmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum density in output (0 means calculate it) </TD></TD>
  79 </TABLE>
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