share/html/online/top.html

   1 <title>top file format</title>
   2 <LINK rel=stylesheet href="style.css" type="text/css">
   3 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
   4 <h2>top file format</h2>
   5 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
   6 <TR>
   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 top file extension stands for topology. It is an ascii file which is
  13 read by <a href="grompp.html">grompp</a> which processes it
  14 and creates a binary topology (<a href="tpb.html">tpb-file</a>).<br>
  15 A sample file is included below:
  16 <pre>
  17 ;
  18 ;       Example topology file
  19 ;
  20 [ defaults ]
  21 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  22   1             1               no              1.0     1.0
  23
  24 ; The force field files to be included
  25 #include "rt41c5.itp"
  26
  27 [ moleculetype ]
  28 ; name  nrexcl
  29 Urea         3
  30
  31 [ atoms ]
  32 ;   nr    type   resnr  residu    atom    cgnr  charge
  33      1       C       1    UREA      C1       1   0.683
  34      2       O       1    UREA      O2       1  -0.683
  35      3      NT       1    UREA      N3       2  -0.622
  36      4       H       1    UREA      H4       2   0.346
  37      5       H       1    UREA      H5       2   0.276
  38      6      NT       1    UREA      N6       3  -0.622
  39      7       H       1    UREA      H7       3   0.346
  40      8       H       1    UREA      H8       3   0.276
  41
  42 [ bonds ]
  43 ;  ai    aj funct           c0           c1
  44     3     4     1 1.000000e-01 3.744680e+05
  45     3     5     1 1.000000e-01 3.744680e+05
  46     6     7     1 1.000000e-01 3.744680e+05
  47     6     8     1 1.000000e-01 3.744680e+05
  48     1     2     1 1.230000e-01 5.020800e+05
  49     1     3     1 1.330000e-01 3.765600e+05
  50     1     6     1 1.330000e-01 3.765600e+05
  51
  52 [ pairs ]
  53 ;  ai    aj funct           c0           c1
  54     2     4     1 0.000000e+00 0.000000e+00
  55     2     5     1 0.000000e+00 0.000000e+00
  56     2     7     1 0.000000e+00 0.000000e+00
  57     2     8     1 0.000000e+00 0.000000e+00
  58     3     7     1 0.000000e+00 0.000000e+00
  59     3     8     1 0.000000e+00 0.000000e+00
  60     4     6     1 0.000000e+00 0.000000e+00
  61     5     6     1 0.000000e+00 0.000000e+00
  62
  63 [ angles ]
  64 ;  ai    aj    ak funct           c0           c1
  65     1     3     4     1 1.200000e+02 2.928800e+02
  66     1     3     5     1 1.200000e+02 2.928800e+02
  67     4     3     5     1 1.200000e+02 3.347200e+02
  68     1     6     7     1 1.200000e+02 2.928800e+02
  69     1     6     8     1 1.200000e+02 2.928800e+02
  70     7     6     8     1 1.200000e+02 3.347200e+02
  71     2     1     3     1 1.215000e+02 5.020800e+02
  72     2     1     6     1 1.215000e+02 5.020800e+02
  73     3     1     6     1 1.170000e+02 5.020800e+02
  74
  75 [ dihedrals ]
  76 ;  ai    aj    ak    al funct           c0           c1           c2
  77     2     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  78     6     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  79     2     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  80     6     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  81     2     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  82     3     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  83     2     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  84     3     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  85
  86 [ dihedrals ]
  87 ;  ai    aj    ak    al funct           c0           c1
  88     3     4     5     1     2 0.000000e+00 1.673600e+02
  89     6     7     8     1     2 0.000000e+00 1.673600e+02
  90     1     3     6     2     2 0.000000e+00 1.673600e+02
  91
  92 ; Include SPC water topology
  93 #include "spc.itp"
  94
  95 [ system ]
  96 Urea in Water
  97
  98 [ molecules ]
  99 Urea    1
 100 SOL     1000
 101 </pre>
 102 <hr>
 103 <div ALIGN=RIGHT>
 104 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 105 </div>
 106 </body>