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   4 <h2>ndx file format</h2>
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   7 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
   8 <TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
   9 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
  10 <TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
  11 <H3>Description</H3>
  12 The GROMACS index file (usually called index.ndx) contains some
  13 user definable sets of atoms. The file can be read by
  14 most analysis programs, by the graphics program (<a href=ngmx.html>ngmx</a>)
  15 and by the preprocessor (<a href=grompp.html>grompp</a>).
  16 Most of these programs create default index groups when no index
  17 file is supplied, so you only need to make an index file when you need special
  18 groups.
  19 <p>
  20 First the group name is written between square brackets.
  21 The following atom numbers may be spread out over as many lines as you like.
  22 The atom numbering starts at 1.
  23 <p>
  24
  25 An example file is here:
  26 <pre>
  27 [ Oxygen ]
  28 1       4       7
  29 [ Hydrogen ]
  30 2       3       5       6
  31 8       9
  32 </pre>
  33
  34 There are two groups, and total nine atoms. The first group
  35 <b>Oxygen</b> has 3 elements.
  36 The second group <b>Hydrogen</b> has 6 elements.
  37 <p>
  38 An index file generation tool is available: <a href=make_ndx.html>make_ndx</a>.
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