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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</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 order parameter per atom for carbon tails. For atom i the
  18 vector i-1, i+1 is used together with an axis.
  19 The index file should contain only the groups to be used for calculations,
  20 with each group of equivalent carbons along the relevant acyl chain in its own
  21 group. There should not be any generic groups (like System, Protein) in the index
  22 file to avoid confusing the program (this is not relevant to tetrahedral order
  23 parameters however, which only work for water anyway).<p>
  24 The program can also give all
  25 diagonal elements of the order tensor and even calculate the deuterium
  26 order parameter Scd (default). If the option -szonly is given, only one
  27 order tensor component (specified by the -d option) is given and the
  28 order parameter per slice is calculated as well. If -szonly is not
  29 selected, all diagonal elements and the deuterium order parameter is
  30 given.<p>The tetrahedrality order parameters can be determined
  31 around an atom. Both angle an distance order parameters are calculated. See
  32 P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
  33 for more details.<br>
  34
  35 <P>
  36 <H3>Files</H3>
  37 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  38 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  39 <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>
  40 <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>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-nr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </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> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  deuter.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-ob</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   eiwit.pdb</a></tt> </TD><TD> Output </TD><TD> Protein data bank file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  sliced.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-Sg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  sg-ang.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-Sk</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sk-dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-Sgsl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg-ang-slice.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-Sksl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sk-dist-slice.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  51 </TABLE>
  52 <P>
  53 <H3>Other options</H3>
  54 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  55 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <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>
  62 <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>
  63 <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>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: <tt>z</tt>, <tt>x</tt> or <tt>y</tt> </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with -d) </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-[no]permolecule</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute per-molecule Scd order parameters </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-[no]radial</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute a radial membrane normal </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-[no]calcdist</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute distance from a reference (currently defined only for radial and permolecule) </TD></TD>
  71 </TABLE>
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