.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
make_ndx - makes index files

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3make_ndx\fP
.BI "\-f" " conf.gro "
.BI "\-n" " index.ndx "
.BI "\-o" " index.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-natoms" " int "
.SH DESCRIPTION
\&Index groups are necessary for almost every gromacs program.
\&All these programs can generate default index groups. You ONLY
\&have to use \fB make_ndx\fR when you need SPECIAL index groups.
\&There is a default index group for the whole system, 9 default
\&index groups for proteins, and a default index group
\&is generated for every other residue name.


\&When no index file is supplied, also \fB make_ndx\fR will generate the
\&default groups.
\&With the index editor you can select on atom, residue and chain names
\&and numbers.
\&When a run input file is supplied you can also select on atom type.
\&You can use NOT, AND and OR, you can split groups
\&into chains, residues or atoms. You can delete and rename groups.


\&The atom numbering in the editor and the index file starts at 1.
.SH FILES
.BI "\-f" " conf.gro" 
.B Input, Opt.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-n" " index.ndx" 
.B Input, Opt., Mult.
 Index file 

.BI "\-o" " index.ndx" 
.B Output
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-natoms"  " int" " 0" 
 set number of atoms (default: read from coordinate or index file)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.