gmx genrestr¶
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-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¶
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-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 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 exclusions.