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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</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 Compute the angle and distance between two groups.
  18 The groups are defined by a number of atoms given in an index file and
  19 may be two or three atoms in size.
  20 If -one is set, only one group should be specified in the index
  21 file and the angle between this group at time 0 and t will be computed.
  22 The angles calculated depend on the order in which the atoms are
  23 given. Giving for instance 5 6 will rotate the vector 5-6 with
  24 180 degrees compared to giving 6 5. <p>If three atoms are given,
  25 the normal on the plane spanned by those three atoms will be
  26 calculated, using the formula  P1P2 x P1P3.
  27 The cos of the angle is calculated, using the inproduct of the two
  28 normalized vectors.<p>
  29 Here is what some of the file options do:<br>
  30 -oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.<br>
  31 -od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.<br>
  32 -od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.<br>
  33 -od2: For two planes this option has no meaning.
  34 <P>
  35 <H3>Files</H3>
  36 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  37 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  38 <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>
  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 </TD><TD> Index file </TD></TR>
  40 <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> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_angle.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sg_dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-od1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_dist1.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-od2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_dist2.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  45 </TABLE>
  46 <P>
  47 <H3>Other options</H3>
  48 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  49 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  50 <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>
  51 <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>
  52 <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>
  53 <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>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Only one group compute angle between vector at time zero and time t </TD></TD>
  59 <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 </TD></TD>
  60 </TABLE>
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