NAME

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

SYNOPSIS

          gmx genrestr [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-o [<.itp>]]
                       [-of [<.ndx>]] [-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 files:

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

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

       Options to specify output files:

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

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

       Other options:

       -fc <vector> (1000 1000 1000)
              Force constants (kJ/mol nm^2)

       -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

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team