table of contents
genrestr(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | genrestr(1) |
NAME¶
genrestr - generates position restraints or distance restraints for index groupsSYNOPSIS¶
genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -[no]version -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -cutoff real -[no]constrDESCRIPTION¶
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. A single isotropic force constant may be given on the command line instead of three components.FILES¶
-f conf.gro InputStructure file: gro g96 pdb tpr etc.
Index file
Include file for topology
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
force constants (kJ/mol nm2)
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
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)
Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |