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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-GENRESTR(1)

gmxgenrestr  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 gmxgenrestr  number
       consecutively  from  1, gmxgenrestr 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 gmxgenrestr.

       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).

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

       Options to specify input files:

       -f[<.gro/.g96/...>](conf.gro)
              Structure file: grog96pdb 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>(100010001000)
              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.

gmx(1)

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

          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]