1 .TH make_ndx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 make_ndx - makes index files
9 .BI "\-n" " index.ndx "
10 .BI "\-o" " index.ndx "
12 .BI "\-[no]version" ""
14 .BI "\-natoms" " int "
16 \&Index groups are necessary for almost every gromacs program.
17 \&All these programs can generate default index groups. You ONLY
18 \&have to use make_ndx when you need SPECIAL index groups.
19 \&There is a default index group for the whole system, 9 default
20 \&index groups are generated for proteins, a default index group
21 \&is generated for every other residue name.
24 \&When no index file is supplied, also make_ndx will generate the
26 \&With the index editor you can select on atom, residue and chain names
28 \&When a run input file is supplied you can also select on atom type.
29 \&You can use NOT, AND and OR, you can split groups
30 \&into chains, residues or atoms. You can delete and rename groups.
33 \&The atom numbering in the editor and the index file starts at 1.
37 Structure file: gro g96 pdb tpr etc.
39 .BI "\-n" " index.ndx"
43 .BI "\-o" " index.ndx"
49 Print help info and quit
51 .BI "\-[no]version" "no "
52 Print version info and quit
54 .BI "\-nice" " int" " 0"
57 .BI "\-natoms" " int" " 0"
58 set number of atoms (default: read from coordinate or index file)
63 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.