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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_cluster can cluster structures with several different methods.
  18 Distances between structures can be determined from a trajectory
  19 or read from an XPM matrix file with the <tt>-dm</tt> option.
  20 RMS deviation after fitting or RMS deviation of atom-pair distances
  21 can be used to define the distance between structures.<p>
  22 single linkage: add a structure to a cluster when its distance to any
  23 element of the cluster is less than <tt>cutoff</tt>.<p>
  24 Jarvis Patrick: add a structure to a cluster when this structure
  25 and a structure in the cluster have each other as neighbors and
  26 they have a least <tt>P</tt> neighbors in common. The neighbors
  27 of a structure are the M closest structures or all structures within
  28 <tt>cutoff</tt>.<p>
  29 Monte Carlo: reorder the RMSD matrix using Monte Carlo.<p>
  30 diagonalization: diagonalize the RMSD matrix.<p>
  31 gromos: use algorithm as described in Daura <it>et al.</it>
  32 (<it>Angew. Chem. Int. Ed.</it> <b>1999</b>, <it>38</it>, pp 236-240).
  33 Count number of neighbors using cut-off, take structure with
  34 largest number of neighbors with all its neighbors as cluster
  35 and eleminate it from the pool of clusters. Repeat for remaining
  36 structures in pool.<p>
  37 When the clustering algorithm assigns each structure to exactly one
  38 cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
  39 file is supplied, the structure with
  40 the smallest average distance to the others or the average structure
  41 or all structures for each cluster will be written to a trajectory
  42 file. When writing all structures, separate numbered files are made
  43 for each cluster.<p>
  44 Two output files are always written:<br>
  45 <tt>-o</tt> writes the RMSD values in the upper left half of the matrix
  46 and a graphical depiction of the clusters in the lower right half
  47 When <tt>-minstruct</tt> = 1 the graphical depiction is black
  48 when two structures are in the same cluster.
  49 When <tt>-minstruct</tt> &gt; 1 different colors will be used for each
  50 cluster.<br>
  51 <tt>-g</tt> writes information on the options used and a detailed list
  52 of all clusters and their members.<p>
  53 Additionally, a number of optional output files can be written:<br>
  54 <tt>-dist</tt> writes the RMSD distribution.<br>
  55 <tt>-ev</tt> writes the eigenvectors of the RMSD matrix
  56 diagonalization.<br>
  57 <tt>-sz</tt> writes the cluster sizes.<br>
  58 <tt>-tr</tt> writes a matrix of the number transitions between
  59 cluster pairs.<br>
  60 <tt>-ntr</tt> writes the total number of transitions to or from
  61 each cluster.<br>
  62 <tt>-clid</tt> writes the cluster number as a function of time.<br>
  63 <tt>-cl</tt> writes average (with option <tt>-av</tt>) or central
  64 structure of each cluster or writes numbered files with cluster members
  65 for a selected set of clusters (with option <tt>-wcl</tt>, depends on
  66 <tt>-nst</tt> and <tt>-rmsmin</tt>).<br>
  67 <P>
  68 <H3>Files</H3>
  69 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  70 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  71 <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, Opt. </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>
  72 <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>
  73 <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>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-dm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    rmsd.xpm</a></tt> </TD><TD> Input, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">rmsd-clust.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> cluster.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-ev</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-eig.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-sz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-size.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-tr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">clust-trans.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-ntr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-trans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-clid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-id.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-cl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">clusters.pdb</a></tt> </TD><TD> Output, Opt. </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>
  84 </TABLE>
  85 <P>
  86 <H3>Other options</H3>
  87 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  88 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  89 <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>
  90 <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>
  91 <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>
  92 <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>
  93 <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>
  94 <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>
  95 <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>
  96 <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>
  97 <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>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMSD matrix in # levels </TD></TD>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1   </tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyze every nr-th frame </TD></TD>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-wcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Write all structures for first # clusters to numbered files </TD></TD>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-nst</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write all structures if more than # per cluster </TD></TD>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-rmsmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> minimum rms difference with rest of cluster for writing structures </TD></TD>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>linkage</tt> </TD><TD> Method for cluster determination: <tt>linkage</tt>, <tt>jarvis-patrick</tt>, <tt>monte-carlo</tt>, <tt>diagonalization</tt> or <tt>gromos</tt> </TD></TD>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-minstruct</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Minimum number of structures in cluster for coloring in the <a href="xpm.html">xpm</a> file </TD></TD>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff </TD></TD>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-M</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff </TD></TD>
 112 <TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of identical nearest neighbors required to form a cluster </TD></TD>
 113 <TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Random number seed for Monte Carlo clustering algorithm </TD></TD>
 114 <TR><TD ALIGN=RIGHT> <b><tt>-niter</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10000</tt> </TD><TD> Number of iterations for MC </TD></TD>
 115 <TR><TD ALIGN=RIGHT> <b><tt>-kT</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) </TD></TD>
 116 </TABLE>
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