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]
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
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
-of option produces an index file that can be used for
freezing atoms. In this case, the input file must be a .pdb file.
-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 to specify input files:
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
Include file for topology
-of[<.ndx>] (freeze.ndx) (Optional)
-fc<vector> (1000 1000 1000)
Force constants (kJ/mol nm^2)
-ofoption 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
Generate a distance restraint matrix for all the atoms in index
Distance range around the actual distance for generating distance restraints
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.
Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)
Only generate distance restraints for atoms pairs within cutoff (nm)
Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.