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GMX-GENRESTR(1) GROMACS GMX-GENRESTR(1) NAME gmx-genrestr - Generate position restraints or distance restraints for index groups SYNOPSIS 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] 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-direc- tion 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, there- fore 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 mol- ecule. 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 gener- ated instead of position restraints. With this matrix, that one typi- cally would apply to Calpha atoms in a protein, one can maintain the overall conformation of a protein without tieing it to a specific posi- tion (as with position restraints). OPTIONS 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-fac- tor 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 dis- tance 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 exclu- sions. SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-GENRESTR(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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