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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_select</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_select writes out basic data about dynamic selections.
  18 It can be used for some simple analyses, or the output can
  19 be combined with output from other programs and/or external
  20 analysis programs to calculate more complex things.
  21 Any combination of the output options is possible, but note
  22 that <tt>-om</tt> only operates on the first selection.<p>
  23 With <tt>-os</tt>, calculates the number of positions in each
  24 selection for each frame. With <tt>-norm</tt>, the output is
  25 between 0 and 1 and describes the fraction from the maximum
  26 number of positions (e.g., for selection 'resname RA and x &lt; 5'
  27 the maximum number of positions is the number of atoms in
  28 RA residues). With <tt>-cfnorm</tt>, the output is divided
  29 by the fraction covered by the selection.
  30 <tt>-norm</tt> and <tt>-cfnorm</tt> can be specified independently
  31 of one another.<p>
  32 With <tt>-oc</tt>, the fraction covered by each selection is
  33 written out as a function of time.<p>
  34 With <tt>-oi</tt>, the selected atoms/residues/molecules are
  35 written out as a function of time. In the output, the first
  36 column contains the frame time, the second contains the number
  37 of positions, followed by the atom/residue/molecule numbers.
  38 If more than one selection is specified, the size of the second
  39 group immediately follows the last number of the first group
  40 and so on. With <tt>-dump</tt>, the frame time and the number
  41 of positions is omitted from the output. In this case, only one
  42 selection can be given.<p>
  43 With <tt>-on</tt>, the selected atoms are written as a index file
  44 compatible with <a href="make_<a href="ndx.html">ndx</a>.html">make_<a href="ndx.html">ndx</a></a> and the analyzing tools. Each selection
  45 is written as a selection group and for dynamic selections a
  46 group is written for each frame.<p>
  47 For residue numbers, the output of <tt>-oi</tt> can be controlled
  48 with <tt>-resnr</tt>: <tt>number</tt> (default) prints the residue
  49 numbers as they appear in the input file, while <tt>index</tt> prints
  50 unique numbers assigned to the residues in the order they appear
  51 in the input file, starting with 1. The former is more intuitive,
  52 but if the input contains multiple residues with the same number,
  53 the output can be less useful.<p>
  54 With <tt>-om</tt>, a mask is printed for the first selection
  55 as a function of time. Each line in the output corresponds to
  56 one frame, and contains either 0/1 for each atom/residue/molecule
  57 possibly selected. 1 stands for the atom/residue/molecule being
  58 selected for the current frame, 0 for not selected.
  59 With <tt>-dump</tt>, the frame time is omitted from the output.
  60 <P>
  61 <H3>Files</H3>
  62 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  63 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  64 <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>
  65 <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>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-sf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">selection.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
  67 <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>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    size.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   cfrac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-oi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">   index.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-om</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">    mask.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-on</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  73 </TABLE>
  74 <P>
  75 <H3>Other options</H3>
  76 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  77 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  78 <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>
  79 <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>
  80 <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>
  81 <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>
  82 <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>
  83 <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>
  84 <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>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-[no]rmpbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Make molecules whole for each frame </TD></TD>
  86 <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 distance calculation </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-select</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Selection string (use 'help' for help) </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-selrpos</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> Selection reference position: <tt>atom</tt>, <tt>res_com</tt>, <tt>res_cog</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>whole_res_com</tt>, <tt>whole_res_cog</tt>, <tt>whole_mol_com</tt>, <tt>whole_mol_cog</tt>, <tt>part_res_com</tt>, <tt>part_res_cog</tt>, <tt>part_mol_com</tt>, <tt>part_mol_cog</tt>, <tt>dyn_res_com</tt>, <tt>dyn_res_cog</tt>, <tt>dyn_mol_com</tt> or <tt>dyn_mol_cog</tt> </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-seltype</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> Default analysis positions: <tt>atom</tt>, <tt>res_com</tt>, <tt>res_cog</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>whole_res_com</tt>, <tt>whole_res_cog</tt>, <tt>whole_mol_com</tt>, <tt>whole_mol_cog</tt>, <tt>part_res_com</tt>, <tt>part_res_cog</tt>, <tt>part_mol_com</tt>, <tt>part_mol_cog</tt>, <tt>dyn_res_com</tt>, <tt>dyn_res_cog</tt>, <tt>dyn_mol_com</tt> or <tt>dyn_mol_cog</tt> </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-[no]dump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Do not print the frame time (-om, -oi) or the index size (-oi) </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Normalize by total number of positions with -os </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-[no]cfnorm</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Normalize by covered fraction with -os </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-resnr</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>number</tt> </TD><TD> Residue number output type: <tt>number</tt> or <tt>index</tt> </TD></TD>
  94 </TABLE>
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