share/html/online/g_bundle.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_bundle</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</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_bundle analyzes bundles of axes. The axes can be for instance
  18 helix axes. The program reads two index groups and divides both
  19 of them in <tt>-na</tt> parts. The centers of mass of these parts
  20 define the tops and bottoms of the axes.
  21 Several quantities are written to file:
  22 the axis length, the distance and the z-shift of the axis mid-points
  23 with respect to the average center of all axes, the total tilt,
  24 the radial tilt and the lateral tilt with respect to the average axis.
  25 <p>
  26 With options <tt>-ok</tt>, <tt>-okr</tt> and <tt>-okl</tt> the total,
  27 radial and lateral kinks of the axes are plotted. An extra index
  28 group of kink atoms is required, which is also divided into <tt>-na</tt>
  29 parts. The kink angle is defined as the angle between the kink-<a href="top.html">top</a> and
  30 the bottom-kink vectors.
  31 <p>
  32 With option <tt>-oa</tt> the <a href="top.html">top</a>, mid (or kink when <tt>-ok</tt> is set)
  33 and bottom points of each axis
  34 are written to a <a href="pdb.html">pdb</a> file each frame. The residue numbers correspond
  35 to the axis numbers. When viewing this file with <tt>rasmol</tt>, use the
  36 command line option <tt>-nmrpdb</tt>, and type <tt>set axis true</tt> to
  37 display the reference axis.
  38 <P>
  39 <H3>Files</H3>
  40 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  41 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  42 <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>
  43 <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>
  44 <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>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bun_len.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_dist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-oz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   bun_z.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tilt.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-otr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tiltr.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-otl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_tiltl.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-ok</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_kink.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-okr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_kinkr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-okl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_kinkl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">    axes.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  55 </TABLE>
  56 <P>
  57 <H3>Other options</H3>
  58 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  59 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  60 <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>
  61 <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>
  62 <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>
  63 <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>
  64 <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>
  65 <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>
  66 <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>
  67 <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>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of axes </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the Z-axis as reference iso the average axis </TD></TD>
  70 </TABLE>
  71 <P>
  72 <hr>
  73 <div ALIGN=RIGHT>
  74 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  75 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  76 </div>
  77 </BODY>