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


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 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 to specify input files:

Structure file: gro g96 pdb brk ent esp tpr
Index file

Options to specify output files:

Include file for topology
Index file

Other options:

Force constants (kJ/mol nm^2)
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
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)
-[no]constr (no)
Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.



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2024, GROMACS development team

January 24, 2024 2023.4