share/html/online/gro.html

   1 <title>gro file format</title>
   2 <body>
   3 <h1>gro file format</h1>
   4
   5 <p>Files with the gro file extension contain a molecular structure in
   6 gromos format. gro files can be used as trajectory by simply
   7 concatenating files. An attempt will be made to read a time value from
   8 the title string in each frame, which should be preceded by
   9 '<TT>t=</TT>', as in the sample below.</p>
  10
  11 <p>A sample piece is included below:
  12 <pre>
  13 MD of 2 waters, t= 0.0
  14     6
  15     1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
  16     1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
  17     1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
  18     2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
  19     2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
  20     2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
  21    1.82060   1.82060   1.82060
  22 </pre>
  23
  24 Lines contain the following information (top to bottom):
  25 <ul>
  26 <li>title string (free format string, optional time in ps after '<TT>t=</TT>')
  27 <li>number of atoms (free format integer)
  28 <li>one line for each atom (fixed format, see below)
  29 <li>box (free format, space separated reals)
  30 </ul>
  31
  32 This format is fixed, ie. all columns are in a fixed
  33 position. Optionally (for now only yet with trjconv) you can write gro
  34 files with any number of decimal places, the format will then be
  35 <tt>n+5</tt> positions with <tt>n</tt> decimal places (<tt>n+1</tt>
  36 for velocities) in stead of <tt>8</tt> with <tt>3</tt> (with
  37 <tt>4</tt> for velicities). Upon reading, the precision will be
  38 inferred from the distance between the decimal points (which will be
  39 <tt>n+5</tt>). Columns contain the following information (from left to
  40 right):
  41
  42 <ul>
  43 <li>residue number (5 positions, integer)
  44 <li>residue name (5 characters)
  45 <li>atom name (5 characters)
  46 <li>atom number (5 positions, integer)
  47 <li>position (in nm, x y z in 3 columns, each 8 positions with 3
  48 decimal places)
  49 <li>velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
  50 decimal places)
  51 </ul>
  52
  53 Note that separate molecules or ions (e.g. water or Cl-) are regarded
  54 as residues.  If you want to write such a file in your own program
  55 without using the GROMACS libraries you can use the following formats:
  56
  57 <dl>
  58 <dt>C format
  59 <dd><tt>"%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"</tt>
  60 <dt>Fortran format
  61 <dd><tt>(i5,2a5,i5,3f8.3,3f8.4)</tt>
  62 <dt>Pascal format
  63 <dd>This is left as an exercise for the user
  64 </dl>
  65 Note that this is the format for writing, as in the above example
  66 fields may be written without spaces, and therefore can not be read
  67 with the same format statement in C.
  68 </body>