DragonFly On-Line Manual Pages

gmx-genrestr(1)                 GROMACS Manual                 gmx-genrestr(1)

NAME
       gmx-genrestr - Generate position restraints or distance restraints for
       index groups

SYNOPSIS
       gmx genrestr [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-o [<.itp>]]
                    [-of [<.ndx>]] [-nice <int>] [-fc <vector>]
                    [-freeze <real>] [-[no]disre] [-disre_dist <real>]
                    [-disre_frac <real>] [-disre_up2 <real>]
                    [-cutoff <real>] [-[no]constr]

DESCRIPTION
       gmx 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 based on the contents of the -f file. A single isotropic
       force constant may be given on the command line instead of three
       components.

       WARNING: Position restraints are interactions within molecules,
       therefore they must be included within the correct [ moleculetype ]
       block in the topology. The atom indices within the [
       position_restraints ] block must be within the range of the atom
       indices for that molecule type. Since the atom numbers in every
       moleculetype in the topology start at 1 and the numbers in the input
       file for gmx genrestr number consecutively from 1, gmx genrestr will
       only produce a useful file for the first molecule. You may wish to edit
       the resulting index file to remove the lines for later atoms, or
       construct a suitable index group to provide as input to gmx genrestr.

       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
       typically 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).

OPTIONS
       Options to specify input and output files:

       -f [<.gro/.g96/...>] (conf.gro) (Input)
           Structure file: gro g96 pdb brk ent esp tpr tpb tpa

       -n [<.ndx>] (index.ndx) (Input, Optional)
           Index file

       -o [<.itp>] (posre.itp) (Output)
           Include file for topology

       -of [<.ndx>] (freeze.ndx) (Output, Optional)
           Index file

       Other options:

       -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]disre  (no)
           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]constr  (no)
           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/>.

VERSION 5.0.6                                                  gmx-genrestr(1)