1GMX-MAKE_NDX(1)                     GROMACS                    GMX-MAKE_NDX(1)
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NAME

6       gmx-make_ndx - Make index files
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SYNOPSIS

9          gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]]
10                       [-natoms <int>] [-[no]twin]
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DESCRIPTION

13       Index groups are necessary for almost every GROMACS program.  All these
14       programs can generate default index groups. You ONLY have  to  use  gmx
15       make_ndx  when you need SPECIAL index groups.  There is a default index
16       group for the whole system, 9 default index groups for proteins, and  a
17       default index group is generated for every other residue name.
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19       When  no  index  file  is supplied, also gmx make_ndx will generate the
20       default groups.  With the index editor you can select on atom,  residue
21       and chain names and numbers.  When a run input file is supplied you can
22       also select on atom type.  You can  use  boolean  operations,  you  can
23       split  groups into chains, residues or atoms. You can delete and rename
24       groups.  Type ‘h’ in the editor for more details.
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26       The atom numbering in the editor and the index file starts at 1.
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28       The -twin switch duplicates all index groups with an offset of -natoms,
29       which  is  useful for Computational Electrophysiology double-layer mem‐
30       brane setups.
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32       See also gmx select -on, which provides an  alternative  way  for  con‐
33       structing index groups.  It covers nearly all of gmx make_ndx function‐
34       ality, and in many cases much more.
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OPTIONS

37       Options to specify input files:
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39       -f [<.gro/.g96/…>] (conf.gro) (Optional)
40              Structure file: gro g96 pdb brk ent esp tpr
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42       -n [<.ndx> […]] (index.ndx) (Optional)
43              Index file
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45       Options to specify output files:
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47       -o [<.ndx>] (index.ndx)
48              Index file
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50       Other options:
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52       -natoms <int> (0)
53              set number of atoms (default:  read  from  coordinate  or  index
54              file)
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56       -[no]twin (no)
57              Duplicate all index groups with an offset of -natoms
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SEE ALSO

60       gmx(1)
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62       More     information    about    GROMACS    is    available    at    <‐
63       http://www.gromacs.org/>.
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66       2019, GROMACS development team
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712019.2                           Apr 16, 2019                  GMX-MAKE_NDX(1)
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