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)

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

NAME

       genrestr - generates position restraints or distance restraints for index groups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       genrestr  -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -[no]version -nice int -fc vector -freeze real -[no]disre -disre_dist
       real -disre_frac real -disre_up2 real -cutoff real -[no]constr

DESCRIPTION

	genrestr produces an include file for a topology containing a list of atom numbers and three  force  constants	for  the    x-,   y-,  and
       z-direction. A single isotropic force constant may be given on the command line instead of three components.

       WARNING:  position  restraints  only work for the one molecule at a time.  Position restraints are interactions within molecules, therefore
       they should be included within the correct  [ moleculetype ] block in the topology. Since the atom numbers in  every  moleculetype  in  the
       topology  start at 1 and the numbers in the input file for  genrestr number consecutively from 1,  genrestr will only produce a useful file
       for the first molecule.

       The  -of option produces an index file that can be used for freezing atoms. In this case, the input file must be a  .pdb file.

       With the  -disre option, half a matrix of distance restraints is generated instead of position restraints. With this matrix, that one typi-
       cally  would  apply  to	Calpha	atoms in a protein, one can maintain the overall conformation of a protein without tieing it to a specific
       position (as with position restraints).

FILES

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

       -n index.ndx Input, Opt.
	Index file

       -o posre.itp Output
	Include file for topology

       -of freeze.ndx Output, Opt.
	Index file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -fc vector 1000 1000 1000
	force constants (kJ/mol nm2)

       -freeze real 0
	if the	-of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less  than
       the level given here

       -[no]disreno
	Generate a distance restraint matrix for all the atoms in index

       -disre_dist real 0.1
	Distance range around the actual distance for generating distance restraints

       -disre_frac real 0
	Fraction  of  distance	to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less
       than the distance given in the previous option, that one is used instead.

       -disre_up2 real 1
	Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)

       -cutoff real -1
	Only generate distance restraints for atoms pairs within cutoff (nm)

       -[no]constrno
	Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       genrestr(1)