g_genrestr_d (1) - Linux Manuals
g_genrestr_d: generates position restraints or distance restraints for index groups
NAMEgenrestr - generates position restraints or distance restraints for index groups
SYNOPSISgenrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -[no]constr
DESCRIPTIONgenrestr produces an include file for a topology containing a list of atom numbers and three force constants for the X, Y and Z direction. A single isotropic force constant may be given on the command line instead of three components.
WARNING: position restraints only work for the one molecule at a time. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ] block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genpr number consecutively from 1, genpr will only produce a useful file for the first molecule.
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 C-alpha atoms in a protein, one can maintain the overall conformation of a protein without tieing it to a specific position (as with position restraints).
FILES-f conf.gro Input
-nice int 0
-fc vector 1000 1000 1000
-freeze real 0
-disre_dist real 0.1
-disre_frac real 0
-disre_up2 real 1
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