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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</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 The structure of liquids can be studied by either neutron or X-ray
  18 scattering. The most common way to describe liquid structure is by a
  19 radial distribution function. However, this is not easy to obtain from
  20 a scattering experiment.<p>
  21 g_rdf calculates radial distribution functions in different ways.
  22 The normal method is around a (set of) particle(s), the other methods
  23 are around the center of mass of a set of particles (<tt>-com</tt>)
  24 or to the closest particle in a set (<tt>-surf</tt>).
  25 With all methods rdf's can also be calculated around axes parallel
  26 to the z-axis with option <tt>-xy</tt>.
  27 With option <tt>-surf</tt> normalization can not be used.<p>
  28 The option <tt>-rdf</tt> sets the type of rdf to be computed.
  29 Default is for atoms or particles, but one can also select center
  30 of mass or geometry of molecules or residues. In all cases only
  31 the atoms in the index groups are taken into account.
  32 For molecules and/or the center of mass option a run input file
  33 is required.
  34 Other weighting than COM or COG can currently only be achieved
  35 by providing a run input file with different masses.
  36 Options <tt>-com</tt> and <tt>-surf</tt> also work in conjunction
  37 with <tt>-rdf</tt>.<p>
  38 If a run input file is supplied (<tt>-s</tt>) and <tt>-rdf</tt> is set
  39 to <tt>atom</tt>, exclusions defined
  40 in that file are taken into account when calculating the rdf.
  41 The option <tt>-cut</tt> is meant as an alternative way to avoid
  42 intramolecular peaks in the rdf plot.
  43 It is however better to supply a run input file with a higher number of
  44 exclusions. For eg. benzene a topology with nrexcl set to 5
  45 would eliminate all intramolecular contributions to the rdf.
  46 Note that all atoms in the selected groups are used, also the ones
  47 that don't have Lennard-Jones interactions.<p>
  48 Option <tt>-cn</tt> produces the cumulative number rdf,
  49 i.e. the average number of particles within a distance r.<p>
  50 To bridge the gap between theory and experiment structure factors can
  51 be computed (option <tt>-sq</tt>). The algorithm uses FFT, the grid
  52 spacing of which is determined by option <tt>-grid</tt>.
  53 <P>
  54 <H3>Files</H3>
  55 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  56 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></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, 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>
  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>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> sfactor.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     rdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-sq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">      sq.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-cn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  rdf_cn.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-hq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">      hq.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  65 </TABLE>
  66 <P>
  67 <H3>Other options</H3>
  68 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  69 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <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>
  75 <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>
  76 <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>
  77 <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>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.002 </tt> </TD><TD> Binwidth (nm) </TD></TD>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-surf</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> RDF with respect to the surface of the first group: <tt>no</tt>, <tt>mol</tt> or <tt>res</tt> </TD></TD>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-rdf</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> RDF type: <tt>atom</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>res_com</tt> or <tt>res_cog</tt> </TD></TD>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge. </TD></TD>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Normalize for volume and density </TD></TD>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-[no]xy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use only the x and y components of the distance </TD></TD>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Shortest distance (nm) to be considered </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of secondary groups to compute RDFs around a central group </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-fade</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done. </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-nlevel</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of different colors in the diffraction image </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-startq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Starting q (1/nm)  </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-endq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>60    </tt> </TD><TD> Ending q (1/nm) </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-energy</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>12    </tt> </TD><TD> Energy of the incoming X-ray (keV)  </TD></TD>
  92 </TABLE>
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