share/html/online/files.html

   1 <TITLE>File formats</TITLE>
   2 <dl>
   3 <dt><h3>Parameter files</h3>
   4 <dl compact>
   5 <a href="mdp.html">mdp</a>
   6 <dd>run parameters, input for
   7 <a href="../programs/gmx-grompp.html">gmx grompp</a> and
   8 <a href="../programs/gmx-convert-tpr.html">gmx convert-tpr</a>
   9 <dt><a href="m2p.html">m2p</a>
  10 <dd>input for <a href="../programs/xpm2ps.html">gmx xpm2ps</a>
  11 </dl>
  12
  13 <br><dt><h3>Structure files</h3>
  14 <dd> <dl compact>
  15 <dt><a href="gro.html">gro</a> <dd>GROMACS format
  16 <dt><a href="g96.html">g96</a> <dd>GROMOS-96 format
  17 <dt><a href="pdb.html">pdb</a> <dd>brookhaven Protein DataBank format
  18 <dt><b>Generic structure formats:</b>
  19 <a href="gro.html">gro</a>,
  20 <a href="g96.html">g96</a>,
  21 <a href="pdb.html">pdb</a>,
  22 <a href="tpr.html">tpr</a>,
  23 <a href="tpb.html">tpb</a> or
  24 <a href="tpa.html">tpa</a>
  25 <dt><b>Structure+mass(db):</b>
  26 <a href="tpr.html">tpr</a>,
  27 <a href="tpb.html">tpb</a>,
  28 <a href="tpa.html">tpa</a>,
  29 <a href="gro.html">gro</a>,
  30 <a href="g96.html">g96</a> or
  31 <a href="pdb.html">pdb</a>.
  32 <dd>Structure and mass input for analysis tools.
  33 When gro or pdb is used approximate masses will be read from the mass database.
  34 </dl>
  35
  36 <br><dt><h3>Topology files</h3>
  37 <dd><dl compact>
  38 <dt><a href="top.html">top</a> <dd>system topology (ascii)
  39 <dt><a href="itp.html">itp</a> <dd>include topology (ascii)
  40 <dt><a href="rtp.html">rtp</a> <dd>residue topology (ascii)
  41 <dt><a href="ndx.html">ndx</a> <dd>index file
  42 </dl>
  43
  44 <br><dt><h3>Run Input files</h3>
  45 <dd><dl compact>
  46 <dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
  47 and velocities (binary, portable)
  48 <dt><a href="tpa.html">tpa</a> <dd>system topology, parameters, coordinates
  49 and velocities (ascii)
  50 <dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates
  51 and velocities (binary)
  52 <dt><b>Generic run input file formats:</b>
  53 <a href="tpr.html">tpr</a>,
  54 <a href="tpb.html">tpb</a> or
  55 <a href="tpa.html">tpa</a>
  56
  57 </dl>
  58
  59 <br><dt><h3>Trajectory files</h3>
  60 <dd><dl compact>
  61 <dt><a href="tng.html">tng</a> <dd>Any kind of data (compressed, portable, any precision)
  62 <dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
  63 <dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
  64 <dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
  65 <dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
  66 <dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
  67 <dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
  68 <dt><b>Formats for full-precision data:</b>
  69 <a href="tng.html">tng</a>,
  70 <a href="trr.html">trr</a> or
  71 <a href="trj.html">trj</a>
  72 <dt><b>Generic trajectory formats:</b>
  73 <a href="tng.html">tng</a>,
  74 <a href="xtc.html">xtc</a>,
  75 <a href="trr.html">trr</a>,
  76 <a href="trj.html">trj</a>,
  77 <a href="gro.html">gro</a>,
  78 <a href="g96.html">g96</a>,
  79 <a href="pdb.html">pdb</a> or
  80 </dl>
  81
  82 <br><dt><h3>Energy files</h3>
  83 <dd><dl compact>
  84 <dt><a href="ene.html">ene</a> <dd>energies, temperature, pressure, box size,
  85 density and virials (binary)
  86 <dt><a href="edr.html">edr</a> <dd>energies, temperature, pressure, box size,
  87 density and virials (binary, portable)
  88 <dt><b>Generic energy formats:</b>
  89 <a href="edr.html">edr</a> or
  90 <a href="ene.html">ene</a>
  91 </dl>
  92
  93 <br><dt><h3>Other files</h3>
  94 <dd><dl compact>
  95 <dt><a href="dat.html">dat</a> <dd>generic, preferred for input
  96 <dt><a href="edi.html">edi</a>
  97 <dd>essential dynamics constraints input for
  98 <a href="../programs/gmx-mdrun.html">gmx mdrun</a>
  99 <dt><a href="edo.html">edo</a>
 100 <dd>essential dynamics constraints output for
 101 <a href="../programs/gmx-mdrun.html">gmx 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
 105 <a href="../programs/gmx-do_dssp.html">gmx do_dssp</a>
 106 <dt><a href="mtx.html">mtx</a> <dd>binary matrix data
 107 <dt><a href="out.html">out</a> <dd>generic, preferred for output
 108 <dt><a href="tex.html">tex</a> <dd>LaTeX input
 109 <dt><a href="xpm.html">xpm</a> <dd>ascii matrix data, use
 110 <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</A> to convert to <a href="eps.html">eps</a>
 111 <dt><a href="xvg.html">xvg</a> <dd>xvgr input
 112 </dl>
 113 </dl>