---
name: "gmx-dyndom"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2019.1-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-dyndom"
---

# gmx-dyndom(1)

Interpolate and extrapolate structure rotations

## NAME

gmx-dyndom - Interpolate and extrapolate structure rotations

## SYNOPSIS

```
gmx dyndom [-f [<.pdb>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
           [-firstangle <real>] [-lastangle <real>] [-nframe <int>]
           [-maxangle <real>] [-trans <real>] [-head <vector>]
           [-tail <vector>]
```

## DESCRIPTION

**gmx dyndom** *reads a .pdb file output from DynDom* *(http://www.cmp.uea.ac.uk/dyndom/).* *It reads the coordinates, the coordinates of the rotation axis,* *and an index file containing the domains.* *Furthermore, it takes the first and last atom of the arrow file* *as command line arguments (head and tail) and* *finally it takes the translation vector (given in DynDom info file)* *and the angle of rotation (also as command line arguments). If the angle* *determined by DynDom is given, one should be able to recover the* *second structure used for generating the DynDom output.* *Because of limited numerical accuracy this should be verified by* *computing an all-atom RMSD (using gmx confrms) rather than by file* *comparison (using diff).*

*The purpose of this program is to interpolate and extrapolate the* *rotation as found by DynDom. As a result unphysical structures with* *long or short bonds, or overlapping atoms may be produced. Visual* *inspection, and energy minimization may be necessary to* *validate the structure.*

## OPTIONS

*Options to specify input files:*

- **-f \[\<.pdb\>\] (dyndom.pdb)**

  *Protein data bank file*

- **-n \[\<.ndx\>\] (domains.ndx)**

  *Index file*

*Options to specify output files:*

- **-o \[\<.xtc/.trr/…\>\] (rotated.xtc)**

  *Trajectory: xtc trr gro g96 pdb tng*

*Other options:*

- **-firstangle \<real\> (0)**

  *Angle of rotation about rotation vector*

- **-lastangle \<real\> (0)**

  *Angle of rotation about rotation vector*

- **-nframe \<int\> (11)**

  *Number of steps on the pathway*

- **-maxangle \<real\> (0)**

  *DymDom dtermined angle of rotation about rotation vector*

- **-trans \<real\> (0)**

  *Translation (Angstrom) along rotation vector (see DynDom info file)*

- **-head \<vector\> (0 0 0)**

  *First atom of the arrow vector*

- **-tail \<vector\> (0 0 0)**

  *Last atom of the arrow vector*

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

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

## COPYRIGHT

*2019, GROMACS development team*