---
name: "genrestr"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-genrestr"
---

# genrestr(1)

Generate position restraints or distance restraints for index groups

Part of [gmx-genrestr(1)](/gmx-genrestr/1.md).

## NAME

gmx-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*-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 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 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.

## SEE ALSO

**[gromacs(7)](/gromacs/7.md)**

More information about **GROMACS** is available at \<*http://www.gromacs.org/*\>.