1make_ndx(1)               GROMACS suite, VERSION 4.5               make_ndx(1)
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NAME

6       make_ndx - makes index files
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8       VERSION 4.5
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SYNOPSIS

11       make_ndx  -f  conf.gro  -n  index.ndx  -o index.ndx -[no]h -[no]version
12       -nice int -natoms int
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DESCRIPTION

15       Index groups are necessary for almost every gromacs program.  All these
16       programs  can  generate  default  index  groups.  You  ONLY have to use
17       make_ndx when you need SPECIAL index groups.  There is a default  index
18       group  for  the  whole system, 9 default index groups are generated for
19       proteins, a default index group is generated for  every  other  residue
20       name.
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23       When no index file is supplied, also make_ndx will generate the default
24       groups.  With the index editor you can  select  on  atom,  residue  and
25       chain  names  and  numbers.   When a run input file is supplied you can
26       also select on atom type.  You can use NOT, AND and OR, you  can  split
27       groups  into  chains,  residues  or  atoms.  You  can delete and rename
28       groups.
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31       The atom numbering in the editor and the index file starts at 1.
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FILES

34       -f conf.gro Input, Opt.
35        Structure file: gro g96 pdb tpr etc.
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37       -n index.ndx Input, Opt., Mult.
38        Index file
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40       -o index.ndx Output
41        Index file
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OTHER OPTIONS

45       -[no]hno
46        Print help info and quit
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48       -[no]versionno
49        Print version info and quit
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51       -nice int 0
52        Set the nicelevel
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54       -natoms int 0
55        set number of atoms (default: read from coordinate or index file)
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SEE ALSO

59       gromacs(7)
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61       More  information  about  GROMACS  is  available  at   <http://www.gro‐
62       macs.org/>.
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66                                Thu 26 Aug 2010                    make_ndx(1)