gmx-genrestr - Man Page

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:

-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.

gmx(1)

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

2024, GROMACS development team

gmx(1).