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:
Options to specify output files:
Other options: