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   1 <TITLE>File formats</TITLE>
   2 <BODY>
   3
   4 <h2>File formats</h2>
   5 <p>
   6 <dl>
   7 <dt>Parameter files:
   8 <dd> <dl compact>
   9 <dt><a href="mdp.html">mdp</a>
  10 <dd>run parameters, input for <a href="grompp.html">grompp</a> and
  11 <a href="tpbconv.html">tpbconv</a>
  12 <dt><a href="m2p.html">m2p</a>
  13 <dd>input for <a href="xpm2ps.html">xpm2ps</a>
  14 </dl>
  15
  16 <br><dt>Structure files:
  17 <dd> <dl compact>
  18 <dt><a href="gro.html">gro</a> <dd>GROMACS format
  19 <dt><a href="g96.html">g96</a> <dd>GROMOS-96 format
  20 <dt><a href="pdb.html">pdb</a> <dd>brookhaven Protein DataBank format
  21 <dt><b>Generic structure format:</b>
  22 <a href="gro.html">gro</a>,
  23 <a href="g96.html">g96</a>,
  24 <a href="pdb.html">pdb</a>,
  25 <a href="tpr.html">tpr</a>,
  26 <a href="tpb.html">tpb</a> or
  27 <a href="tpa.html">tpa</a>
  28 <dt><b>Structure+mass(db):</b>
  29 <a href="tpr.html">tpr</a>,
  30 <a href="tpb.html">tpb</a>,
  31 <a href="tpa.html">tpa</a>,
  32 <a href="gro.html">gro</a>,
  33 <a href="g96.html">g96</a> or
  34 <a href="pdb.html">pdb</a>.
  35 <dd>Structure and mass input for analysis tools.
  36 When gro or pdb is used approximate masses will be read from the mass database.
  37 </dl>
  38
  39 <br><dt>Topology files:
  40 <dd><dl compact>
  41 <dt><a href="top.html">top</a> <dd>system topology (ascii)
  42 <dt><a href="itp.html">itp</a> <dd>include topology (ascii)
  43 <dt><a href="rtp.html">rtp</a> <dd>residue topology (ascii)
  44 <dt><a href="ndx.html">ndx</a> <dd>index file
  45 </dl>
  46
  47 <br><dt>Run Input files:
  48 <dd><dl compact>
  49 <dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
  50 and velocities (binary, portable)
  51 <dt><a href="tpa.html">tpa</a> <dd>system topology, parameters, coordinates
  52 and velocities (ascii)
  53 <dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates
  54 and velocities (binary)
  55 <dt><b>Generic run input file format:</b>
  56 <a href="tpr.html">tpr</a>,
  57 <a href="tpb.html">tpb</a> or
  58 <a href="tpa.html">tpa</a>
  59
  60 </dl>
  61
  62 <br><dt>Trajectory files:
  63 <dd><dl compact>
  64 <dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
  65 <dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
  66 <dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
  67 <dt><a href="g87.html">g87</a> <dd>x and v (ascii)
  68 <dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
  69 <dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
  70 <dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
  71 <dt><b>Full precision format:</b>
  72 <a href="trr.html">trr</a> or
  73 <a href="trj.html">trj</a>
  74 <dt><b>Generic trajectory format:</b>
  75 <a href="xtc.html">xtc</a>,
  76 <a href="trr.html">trr</a>,
  77 <a href="trj.html">trj</a>,
  78 <a href="gro.html">gro</a>,
  79 <a href="g96.html">g96</a>,
  80 <a href="pdb.html">pdb</a> or
  81 <a href="g87.html">g87</a>
  82 </dl>
  83
  84 <br><dt>Energy files:
  85 <dd><dl compact>
  86 <dt><a href="ene.html">ene</a> <dd>energies, temperature, pressure, box size,
  87 density and virials (binary)
  88 <dt><a href="edr.html">edr</a> <dd>energies, temperature, pressure, box size,
  89 density and virials (binary, portable)
  90 <dt><b>Generic energy format:</b>
  91 <a href="edr.html">edr</a> or
  92 <a href="ene.html">ene</a>
  93 </dl>
  94
  95 <br><dt>Other files:
  96 <dd><dl compact>
  97 <dt><a href="dat.html">dat</a> <dd>generic, preferred for input
  98 <dt><a href="edi.html">edi</a>
  99 <dd>essential dynamics constraints input for <a href="mdrun.html">mdrun</a>
 100 <dt><a href="edo.html">edo</a>
 101 <dd>essential dynamics constraints output for <a href="mdrun.html">mdrun</a>
 102 <dt><a href="eps.html">eps</a> <dd>Encapsulated Postscript
 103 <dt><a href="log.html">log</a> <dd>log file
 104 <dt><a href="map.html">map</a> <dd>colormap input for <a href="do_dssp.html">do_dssp</a>
 105 <dt><a href="mtx.html">mtx</a> <dd>binary matrix data
 106 <dt><a href="out.html">out</a> <dd>generic, preferred for output
 107 <dt><a href="tex.html">tex</a> <dd>LaTeX input
 108 <dt><a href="xpm.html">xpm</a> <dd>ascii matrix data, use <a href="xpm2ps.html">xpm2ps</A> to convert to <a href="eps.html">eps</a>
 109 <dt><a href="xvg.html">xvg</a> <dd>xvgr input
 110 </dl>
 111 </dl>
 112
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