share/html/online/files.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>File formats</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>File Formats</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 4.0<br>
  13 Sun 18 Jan 2009</B></td></tr></TABLE>
  14 <HR>
  15 <dl>
  16 <dt><h3>Parameter files</h3>
  17 <dl compact>
  18 <a href="mdp.html">mdp</a>
  19 <dd>run parameters, input for <a href="grompp.html">grompp</a> and
  20 <a href="tpbconv.html">tpbconv</a>
  21 <dt><a href="m2p.html">m2p</a>
  22 <dd>input for <a href="xpm2ps.html">xpm2ps</a>
  23 </dl>
  24
  25 <br><dt><h3>Structure files</h3>
  26 <dd> <dl compact>
  27 <dt><a href="gro.html">gro</a> <dd>GROMACS format
  28 <dt><a href="g96.html">g96</a> <dd>GROMOS-96 format
  29 <dt><a href="pdb.html">pdb</a> <dd>brookhaven Protein DataBank format
  30 <dt><b>Generic structure formats:</b>
  31 <a href="gro.html">gro</a>,
  32 <a href="g96.html">g96</a>,
  33 <a href="pdb.html">pdb</a>,
  34 <a href="tpr.html">tpr</a>,
  35 <a href="tpb.html">tpb</a> or
  36 <a href="tpa.html">tpa</a>
  37 <dt><b>Structure+mass(db):</b>
  38 <a href="tpr.html">tpr</a>,
  39 <a href="tpb.html">tpb</a>,
  40 <a href="tpa.html">tpa</a>,
  41 <a href="gro.html">gro</a>,
  42 <a href="g96.html">g96</a> or
  43 <a href="pdb.html">pdb</a>.
  44 <dd>Structure and mass input for analysis tools.
  45 When gro or pdb is used approximate masses will be read from the mass database.
  46 </dl>
  47
  48 <br><dt><h3>Topology files</h3>
  49 <dd><dl compact>
  50 <dt><a href="top.html">top</a> <dd>system topology (ascii)
  51 <dt><a href="itp.html">itp</a> <dd>include topology (ascii)
  52 <dt><a href="rtp.html">rtp</a> <dd>residue topology (ascii)
  53 <dt><a href="ndx.html">ndx</a> <dd>index file
  54 </dl>
  55
  56 <br><dt><h3>Run Input files</h3>
  57 <dd><dl compact>
  58 <dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
  59 and velocities (binary, portable)
  60 <dt><a href="tpa.html">tpa</a> <dd>system topology, parameters, coordinates
  61 and velocities (ascii)
  62 <dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates
  63 and velocities (binary)
  64 <dt><b>Generic run input file formats:</b>
  65 <a href="tpr.html">tpr</a>,
  66 <a href="tpb.html">tpb</a> or
  67 <a href="tpa.html">tpa</a>
  68
  69 </dl>
  70
  71 <br><dt><h3>Trajectory files</h3>
  72 <dd><dl compact>
  73 <dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
  74 <dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
  75 <dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
  76 <dt><a href="g87.html">g87</a> <dd>x and v (ascii)
  77 <dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
  78 <dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
  79 <dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
  80 <dt><b>Full precision formats:</b>
  81 <a href="trr.html">trr</a> or
  82 <a href="trj.html">trj</a>
  83 <dt><b>Generic trajectory formats:</b>
  84 <a href="xtc.html">xtc</a>,
  85 <a href="trr.html">trr</a>,
  86 <a href="trj.html">trj</a>,
  87 <a href="gro.html">gro</a>,
  88 <a href="g96.html">g96</a>,
  89 <a href="pdb.html">pdb</a> or
  90 <a href="g87.html">g87</a>
  91 </dl>
  92
  93 <br><dt><h3>Energy files</h3>
  94 <dd><dl compact>
  95 <dt><a href="ene.html">ene</a> <dd>energies, temperature, pressure, box size,
  96 density and virials (binary)
  97 <dt><a href="edr.html">edr</a> <dd>energies, temperature, pressure, box size,
  98 density and virials (binary, portable)
  99 <dt><b>Generic energy formats:</b>
 100 <a href="edr.html">edr</a> or
 101 <a href="ene.html">ene</a>
 102 </dl>
 103
 104 <br><dt><h3>Other files</h3>
 105 <dd><dl compact>
 106 <dt><a href="dat.html">dat</a> <dd>generic, preferred for input
 107 <dt><a href="edi.html">edi</a>
 108 <dd>essential dynamics constraints input for <a href="mdrun.html">mdrun</a>
 109 <dt><a href="edo.html">edo</a>
 110 <dd>essential dynamics constraints output for <a href="mdrun.html">mdrun</a>
 111 <dt><a href="eps.html">eps</a> <dd>Encapsulated Postscript
 112 <dt><a href="log.html">log</a> <dd>log file
 113 <dt><a href="map.html">map</a> <dd>colormap input for <a href="do_dssp.html">do_dssp</a>
 114 <dt><a href="mtx.html">mtx</a> <dd>binary matrix data
 115 <dt><a href="out.html">out</a> <dd>generic, preferred for output
 116 <dt><a href="tex.html">tex</a> <dd>LaTeX input
 117 <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>
 118 <dt><a href="xvg.html">xvg</a> <dd>xvgr input
 119 </dl>
 120 </dl>
 121 <hr>
 122 <div ALIGN=RIGHT>
 123 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 124 </div>
 125
 126 </BODY>