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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</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_sorient analyzes solvent orientation around solutes.
  18 It calculates two angles between the vector from one or more
  19 reference positions to the first atom of each solvent molecule:<br>
  20 theta1: the angle with the vector from the first atom of the solvent
  21 molecule to the midpoint between atoms 2 and 3.<br>
  22 theta2: the angle with the normal of the solvent plane, defined by the
  23 same three atoms, or when the option <tt>-v23</tt> is set
  24 the angle with the vector between atoms 2 and 3.<br>
  25 The reference can be a set of atoms or
  26 the center of mass of a set of atoms. The group of solvent atoms should
  27 consist of 3 atoms per solvent molecule.
  28 Only solvent molecules between <tt>-rmin</tt> and <tt>-rmax</tt> are
  29 considered for <tt>-o</tt> and <tt>-no</tt> each frame.<p>
  30 <tt>-o</tt>: distribtion of cos(theta1) for rmin&lt;=r&lt;=rmax.<p>
  31 <tt>-no</tt>: distribution of cos(theta2) for rmin&lt;=r&lt;=rmax.<p>
  32 <tt>-ro</tt>: &lt;cos(theta1)&gt; and &lt;3cos^2(theta2)-1&gt; as a function of the
  33 distance.<p>
  34 <tt>-co</tt>: the sum over all solvent molecules within distance r
  35 of cos(theta1) and 3cos^2(theta2)-1 as a function of r.<p>
  36 <tt>-rc</tt>: the distribution of the solvent molecules as a function of r
  37 <P>
  38 <H3>Files</H3>
  39 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  40 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  41 <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>
  42 <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>
  43 <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>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    sori.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    snor.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-ro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    sord.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    scum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-rc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  scount.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>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v23</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the vector between atoms 2 and 3 </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Minimum distance (nm) </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Maximum distance (nm) </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-cbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02  </tt> </TD><TD> Binwidth for the cosine </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02  </tt> </TD><TD> Binwidth for r (nm) </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. </TD></TD>
  69 </TABLE>
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