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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotmat</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-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 g_rotmat plots the rotation matrix required for least squares fitting
  18 a conformation onto the reference conformation provided with
  19 <tt>-s</tt>. Translation is removed before fitting.
  20 The output are the three vectors that give the new directions
  21 of the x, y and z directions of the reference conformation,
  22 for example: (zx,zy,zz) is the orientation of the reference
  23 z-axis in the trajectory frame.
  24 <p>
  25 This tool is useful for, for instance,
  26 determining the orientation of a molecule
  27 at an interface, possibly on a trajectory produced with
  28 <tt><a href="trjconv.html">trjconv</a> -fit rotxy+transxy</tt> to remove the rotation
  29 in the xy-plane.
  30 <p>
  31 Option <tt>-ref</tt> determines a reference structure for fitting,
  32 instead of using the structure from <tt>-s</tt>. The structure with
  33 the lowest sum of RMSD's to all other structures is used.
  34 Since the computational cost of this procedure grows with
  35 the square of the number of frames, the <tt>-skip</tt> option
  36 can be useful. A full fit or only a fit in the x/y plane can
  37 be performed.
  38 <p>
  39 Option <tt>-fitxy</tt> fits in the x/y plane before determining
  40 the rotation matrix.
  41 <P>
  42 <H3>Files</H3>
  43 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  44 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  45 <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>
  46 <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>
  47 <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>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  rotmat.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  49 </TABLE>
  50 <P>
  51 <H3>Other options</H3>
  52 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  53 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  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>-ref</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Determine the optimal reference structure: <tt>none</tt>, <tt>xyz</tt> or <tt>xy</tt> </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Use every nr-th frame for -ref </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fitxy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Fit the x/y rotation before determining the rotation </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use mass weighted fitting </TD></TD>
  66 </TABLE>
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