1GMX-GENRESTR(1) GROMACS GMX-GENRESTR(1)
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6 gmx-genrestr - Generate position restraints or distance restraints for
7 index groups
8
10 gmx genrestr [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-o [<.itp>]]
11 [-of [<.ndx>]] [-fc <vector>] [-freeze <real>]
12 [-[no]disre] [-disre_dist <real>] [-disre_frac <real>]
13 [-disre_up2 <real>] [-cutoff <real>] [-[no]constr]
14
16 gmx genrestr produces an #include file for a topology containing a list
17 of atom numbers and three force constants for the x-, y-, and z-direc‐
18 tion based on the contents of the -f file. A single isotropic force
19 constant may be given on the command line instead of three components.
20 WARNING: Position restraints are interactions within molecules, there‐
22 fore they must be included within the correct [ moleculetype ] block in
23 the topology. The atom indices within the [ position_restraints ] block
24 must be within the range of the atom indices for that molecule type.
25 Since the atom numbers in every moleculetype in the topology start at 1
26 and the numbers in the input file for gmx genrestr number consecutively
27 from 1, gmx genrestr will only produce a useful file for the first mol‐
28 ecule. You may wish to edit the resulting index file to remove the
29 lines for later atoms, or construct a suitable index group to provide
30 as input to gmx genrestr.
31 The -of option produces an index file that can be used for freezing
33 atoms. In this case, the input file must be a .pdb file.
34 With the -disre option, half a matrix of distance restraints is gener‐
36 ated instead of position restraints. With this matrix, that one typi‐
37 cally would apply to Calpha atoms in a protein, one can maintain the
38 overall conformation of a protein without tieing it to a specific posi‐
39 tion (as with position restraints).
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42 Options to specify input files:
43 -f [<.gro/.g96/…>] (conf.gro)
45 Structure file: gro g96 pdb brk ent esp tpr
46 -n [<.ndx>] (index.ndx) (Optional)
48 Index file
49 Options to specify output files:
51 -o [<.itp>] (posre.itp)
53 Include file for topology
54 -of [<.ndx>] (freeze.ndx) (Optional)
56 Index file
57 Other options:
59 -fc <vector> (1000 1000 1000)
61 Force constants (kJ/mol nm^2)
62 -freeze <real> (0)
64 If the -of option or this one is given an index file will be
65 written containing atom numbers of all atoms that have a B-fac‐
66 tor less than the level given here
67 -[no]disre (no)
69 Generate a distance restraint matrix for all the atoms in index
70 -disre_dist <real> (0.1)
72 Distance range around the actual distance for generating dis‐
73 tance restraints
74 -disre_frac <real> (0)
76 Fraction of distance to be used as interval rather than a fixed
77 distance. If the fraction of the distance that you specify here
78 is less than the distance given in the previous option, that one
79 is used instead.
80 -disre_up2 <real> (1)
82 Distance between upper bound for distance restraints, and the
83 distance at which the force becomes constant (see manual)
84 -cutoff <real> (-1)
86 Only generate distance restraints for atoms pairs within cutoff
87 (nm)
88 -[no]constr (no)
90 Generate a constraint matrix rather than distance restraints.
91 Constraints of type 2 will be generated that do generate exclu‐
92 sions.
93
95 gmx(1)
96 More information about GROMACS is available at <‐
98 http://www.gromacs.org/>.
99
101 2020, GROMACS development team
1022019.6 Feb 28, 2020 GMX-GENRESTR(1)