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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_vanhove</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 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 g_vanhove computes the Van Hove correlation function.
  18 The Van Hove G(r,t) is the probability that a particle that is at r0
  19 at time zero can be found at position r0+r at time t.
  20 g_vanhove determines G not for a vector r, but for the length of r.
  21 Thus it gives the probability that a particle moves a distance of r
  22 in time t.
  23 Jumps across the periodic boundaries are removed.
  24 Corrections are made for scaling due to isotropic
  25 or anisotropic pressure coupling.
  26 <p>
  27 With option <tt>-om</tt> the whole matrix can be written as a function
  28 of t and r or as a function of sqrt(t) and r (option <tt>-sqrt</tt>).
  29 <p>
  30 With option <tt>-or</tt> the Van Hove function is plotted for one
  31 or more values of t. Option <tt>-nr</tt> sets the number of times,
  32 option <tt>-fr</tt> the number spacing between the times.
  33 The binwidth is set with option <tt>-rbin</tt>. The number of bins
  34 is determined automatically.
  35 <p>
  36 With option <tt>-ot</tt> the integral up to a certain distance
  37 (option <tt>-rt</tt>) is plotted as a function of time.
  38 <p>
  39 For all frames that are read the coordinates of the selected particles
  40 are stored in memory. Therefore the program may use a lot of memory.
  41 For options <tt>-om</tt> and <tt>-ot</tt> the program may be slow.
  42 This is because the calculation scales as the number of frames times
  43 <tt>-fm</tt> or <tt>-ft</tt>.
  44 Note that with the <tt>-dt</tt> option the memory usage and calculation
  45 time can be reduced.
  46 <P>
  47 <H3>Files</H3>
  48 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  49 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  50 <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>
  51 <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> 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>
  52 <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>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-om</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> vanhove.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">vanhove_r.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">vanhove_t.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr 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> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  63 <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>
  64 <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>
  65 <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>
  66 <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>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_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>
  68 <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>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-sqrt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps) </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-fm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames in the matrix, 0 is plot all </TD></TD>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>2     </tt> </TD><TD> Maximum r in the matrix (nm) </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.01  </tt> </TD><TD> Binwidth in the matrix and for -or (nm) </TD></TD>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-mmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum density in the matrix, 0 is calculate (1/nm) </TD></TD>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>81</tt> </TD><TD> Number of levels in the matrix </TD></TD>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-nr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of curves for the -or output </TD></TD>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-fr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Frame spacing for the -or output </TD></TD>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-rt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Integration limit for the -ot output (nm) </TD></TD>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-ft</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames in the -ot output, 0 is plot all </TD></TD>
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