1GMX-GENRESTR(1)                     GROMACS                    GMX-GENRESTR(1)
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NAME

6       gmx-genrestr  - Generate position restraints or distance restraints for
7       index groups
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SYNOPSIS

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]
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DESCRIPTION

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.
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21       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.
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32       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.
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35       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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OPTIONS

42       Options to specify input files:
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44       -f [<.gro/.g96/…>] (conf.gro)
45              Structure file: gro g96 pdb brk ent esp tpr
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47       -n [<.ndx>] (index.ndx) (Optional)
48              Index file
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50       Options to specify output files:
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52       -o [<.itp>] (posre.itp)
53              Include file for topology
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55       -of [<.ndx>] (freeze.ndx) (Optional)
56              Index file
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58       Other options:
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60       -fc <vector> (1000 1000 1000)
61              Force constants (kJ/mol nm^2)
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63       -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
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68       -[no]disre (no)
69              Generate a distance restraint matrix for all the atoms in index
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71       -disre_dist <real> (0.1)
72              Distance  range  around  the actual distance for generating dis‐
73              tance restraints
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75       -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.
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81       -disre_up2 <real> (1)
82              Distance  between  upper  bound for distance restraints, and the
83              distance at which the force becomes constant (see manual)
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85       -cutoff <real> (-1)
86              Only generate distance restraints for atoms pairs within  cutoff
87              (nm)
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89       -[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.
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SEE ALSO

95       gmx(1)
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97       More     information    about    GROMACS    is    available    at    <‐
98       http://www.gromacs.org/>.
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101       2019, GROMACS development team
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1062019.4                           Oct 02, 2019                  GMX-GENRESTR(1)
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