Login or Register to Ask a Question and Join Our Community

Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

make_ndx(1) [debian man page]

make_ndx(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       make_ndx(1)

NAME

       make_ndx - makes index files

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

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

DESCRIPTION

       Index  groups  are  necessary for almost every gromacs program.	All these programs can generate default index groups. You ONLY have to use
       make_ndx 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  make_ndx 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.

FILES

       -f conf.gro Input, Opt.
	Structure file: gro g96 pdb tpr etc.

       -n index.ndx Input, Opt., Mult.
	Index file

       -o index.ndx Output
	Index file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

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

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       make_ndx(1)

Check Out this Related Man Page

g_principal(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				    g_principal(1)

NAME

       g_principal - calculates axes of inertia for a group of atoms

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_principal  -f	traj.xtc  -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -[no]version -nice int -b
       time -e time -dt time -tu enum -[no]w -[no]foo

DESCRIPTION

	g_principal calculates the three principal axes of inertia for a group of atoms.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -a1 axis1.dat Output
	Generic data file

       -a2 axis2.dat Output
	Generic data file

       -a3 axis3.dat Output
	Generic data file

       -om moi.dat Output
	Generic data file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -tu enum ps
	Time unit:  fs,  ps,  ns,  us,	ms or  s

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]foono
	Dummy option to avoid empty array

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						    g_principal(1)
Man Page