.. _gmx genrestr: gmx genrestr ============ Synopsis -------- .. parsed-literal:: gmx genrestr [:strong:`-f` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.itp>]`] [:strong:`-of` :emphasis:`[<.ndx>]`] [:strong:`-fc` :emphasis:``] [:strong:`-freeze` :emphasis:``] [:strong:`-[no]disre`] [:strong:`-disre_dist` :emphasis:``] [:strong:`-disre_frac` :emphasis:``] [:strong:`-disre_up2` :emphasis:``] [:strong:`-cutoff` :emphasis:``] [:strong:`-[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 :ref:`.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: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`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`` (1000 1000 1000) Force constants (kJ/mol nm^2) ``-freeze`` (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`` (0.1) Distance range around the actual distance for generating distance restraints ``-disre_frac`` (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`` (1) Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual) ``-cutoff`` (-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. .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at .