gmx-genrestr(1) GROMACS Manual gmx-genrestr(1)NAMEgmx-genrestr - Generate position restraints or distance restraints for
index groups
SYNOPSIS
gmx genrestr [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-o [<.itp>]]
[-of [<.ndx>]] [-nice <int>] [-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 and output files:
-f [<.gro/.g96/...>] (conf.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.itp>] (posre.itp) (Output)
Include file for topology
-of [<.ndx>] (freeze.ndx) (Output, Optional)
Index file
Other options:
-nice <int> (0)
Set the nicelevel
-fc <vector> (1000 1000 1000)
Force constants (kJ/mol nm2)
-freeze <real> (0)
If the -of option or this one is given an index file will be writ‐
ten 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 dis‐
tance 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. Con‐
straints of type 2 will be generated that do generate exclusions.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-genrestr(1)
