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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</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 genconf multiplies a given coordinate file by simply stacking them
  18 on <a href="top.html">top</a> of each other, like a small child playing with wooden blocks.
  19 The program makes a grid of <it>user defined</it>
  20 proportions (<tt>-nbox</tt>),
  21 and interspaces the grid point with an extra space <tt>-dist</tt>.<p>
  22 When option <tt>-rot</tt> is used the program does not check for overlap
  23 between molecules on grid points. It is recommended to make the box in
  24 the input file at least as big as the coordinates +
  25 Van der Waals radius.<p>
  26 If the optional trajectory file is given, conformations are not
  27 generated, but read from this file and translated appropriately to
  28 build the grid.
  29 <P>
  30 <H3>Files</H3>
  31 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  32 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  33 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">     out.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-trj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input, Opt. </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>
  36 </TABLE>
  37 <P>
  38 <H3>Other options</H3>
  39 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  40 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  41 <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>
  42 <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>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-nbox</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Number of boxes </TD></TD>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Distance between boxes </TD></TD>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random generator seed, if 0 generated from the time </TD></TD>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Randomly rotate conformations </TD></TD>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Random shuffling of molecules </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Sort molecules on X coord </TD></TD>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Divide the box in blocks on this number of cpus </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-nmolat</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system! </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-maxrot</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>180 180 180</tt> </TD><TD> Maximum random rotation </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Renumber residues </TD></TD>
  54 </TABLE>
  55 <P>
  56 <H3>Known problems</H3>
  57 <UL>
  58 <LI>The program should allow for random displacement of lattice points.
  59 </UL>
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