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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_clustsize</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 This program computes the size distributions of molecular/atomic clusters in
  18 the gas phase. The output is given in the form of a XPM file.
  19 The total number of clusters is written to a XVG file.<p>
  20 When the <tt>-mol</tt> option is given clusters will be made out of
  21 molecules rather than atoms, which allows clustering of large molecules.
  22 In this case an index file would still contain atom numbers
  23 or your calculation will die with a SEGV.<p>
  24 When velocities are present in your trajectory, the temperature of
  25 the largest cluster will be printed in a separate <a href="xvg.html">xvg</a> file assuming
  26 that the particles are free to move. If you are using constraints,
  27 please correct the temperature. For instance water simulated with SHAKE
  28 or SETTLE will yield a temperature that is 1.5 times too low. You can
  29 compensate for this with the -ndf option. Remember to take the removal
  30 of center of mass motion into account.<p>
  31 The <tt>-mc</tt> option will produce an index file containing the
  32 atom numbers of the largest cluster.
  33 <P>
  34 <H3>Files</H3>
  35 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  36 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  37 <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>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="tpr.html">   topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Portable xdr run input file </TD></TR>
  39 <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>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">   csize.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-ow</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">  csizew.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-nc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  nclust.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-mc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">maxclust.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-ac</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> avclust.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-hc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">histo-clust.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    temp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-mcn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">maxclust.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  48 </TABLE>
  49 <P>
  50 <H3>Other options</H3>
  51 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  52 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  53 <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>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
  60 <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>
  61 <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>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.35  </tt> </TD><TD> Largest distance (nm) to be considered in a cluster </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Cluster molecules rather than atoms (needs <a href="tpr.html">tpr</a> file) </TD></TD>
  64 <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 </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-nskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of frames to skip between writing </TD></TD>
  66 <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 levels of grey in <a href="xpm.html">xpm</a> output </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-ndf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used. </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-rgblo</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 0</tt> </TD><TD> RGB values for the color of the lowest occupied cluster size </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-rgbhi</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 1</tt> </TD><TD> RGB values for the color of the highest occupied cluster size </TD></TD>
  70 </TABLE>
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