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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_polystat</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 g_polystat plots static properties of polymers as a function of time
  18 and prints the average.<p>
  19 By default it determines the average end-to-end distance and radii
  20 of gyration of polymers. It asks for an index group and split this
  21 into molecules. The end-to-end distance is then determined using
  22 the first and the last atom in the index group for each molecules.
  23 For the radius of gyration the total and the three principal components
  24 for the average gyration tensor are written.
  25 With option <tt>-v</tt> the eigenvectors are written.
  26 With option <tt>-pc</tt> also the average eigenvalues of the individual
  27 gyration tensors are written.
  28 With option <tt>-i</tt> the mean square internal distances are
  29 written.<p>
  30 With option <tt>-p</tt> the persistence length is determined.
  31 The chosen index group should consist of atoms that are
  32 consecutively bonded in the polymer mainchains.
  33 The persistence length is then determined from the cosine of
  34 the angles between bonds with an index difference that is even,
  35 the odd pairs are not used, because straight polymer backbones
  36 are usually all trans and therefore only every second bond aligns.
  37 The persistence length is defined as number of bonds where
  38 the average cos reaches a value of 1/e. This point is determined
  39 by a linear interpolation of <a href="log.html">log</a>(&lt;cos&gt;).
  40 <P>
  41 <H3>Files</H3>
  42 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  43 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  44 <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>
  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>-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>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">polystat.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> polyvec.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> persist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> intdist.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>-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>
  63 <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>
  64 <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>
  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 the mass weighting for radii of gyration </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Plot average eigenvalues </TD></TD>
  67 </TABLE>
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