debian man page for genrestr

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)