---
name: "gmx-helix"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-helix"
---

# gmx-helix(1)

Calculate basic properties of alpha helices

## NAME

gmx-helix - Calculate basic properties of alpha helices

## SYNOPSIS

```
gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
          [-cz [<.gro/.g96/...>]] [-b <time>] [-e <time>]
          [-dt <time>] [-[no]w] [-r0 <int>] [-[no]q] [-[no]F]
          [-[no]db] [-[no]ev] [-ahxstart <int>] [-ahxend <int>]
```

## DESCRIPTION

**gmx helix** computes all kinds of helix properties. First, the peptide is checked to find the longest helical part, as determined by hydrogen bonds and phi/psi angles. That bit is fitted to an ideal helix around the *z*-axis and centered around the origin. Then the following properties are computed:

- •

  Helix radius (file **radius.xvg**). This is merely the RMS deviation in two dimensions for all Calpha atoms. it is calculated as sqrt((sum\_i (x^2(i)+y^2(i)))/N) where N is the number of backbone atoms. For an ideal helix the radius is 0.23 nm.

- •

  Twist (file **twist.xvg**). The average helical angle per residue is calculated. For an alpha-helix it is 100 degrees, for 3-10 helices it will be smaller, and for 5-helices it will be larger.

- •

  Rise per residue (file **rise.xvg**). The helical rise per residue is plotted as the difference in *z*-coordinate between Calpha atoms. For an ideal helix, this is 0.15 nm.

- •

  Total helix length (file **len-ahx.xvg**). The total length of the helix in nm. This is simply the average rise (see above) times the number of helical residues (see below).

- •

  Helix dipole, backbone only (file **dip-ahx.xvg**).

- •

  RMS deviation from ideal helix, calculated for the Calpha atoms only (file **rms-ahx.xvg**).

- •

  Average Calpha - Calpha dihedral angle (file **phi-ahx.xvg**).

- •

  Average phi and psi angles (file **phipsi.xvg**).

- •

  Ellipticity at 222 nm according to Hirst and Brooks.

## OPTIONS

Options to specify input files:

- **-s \[\<.tpr\>\] (topol.tpr)**

  Portable xdr run input file

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

  Index file

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  Trajectory: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

Options to specify output files:

- **-cz \[\<.gro/.g96/...\>\] (zconf.gro)**

  Structure file: *gro* *g96* *pdb* brk ent esp

Other options:

- **-b \<time\> (0)**

  Time of first frame to read from trajectory (default unit ps)

- **-e \<time\> (0)**

  Time of last frame to read from trajectory (default unit ps)

- **-dt \<time\> (0)**

  Only use frame when t MOD dt = first time (default unit ps)

- **-\[no\]w (no)**

  View output *.xvg*, *.xpm*, *.eps* and *.pdb* files

- **-r0 \<int\> (1)**

  The first residue number in the sequence

- **-\[no\]q (no)**

  Check at every step which part of the sequence is helical

- **-\[no\]F (yes)**

  Toggle fit to a perfect helix

- **-\[no\]db (no)**

  Print debug info

- **-\[no\]ev (no)**

  Write a new 'trajectory' file for ED

- **-ahxstart \<int\> (0)**

  First residue in helix

- **-ahxend \<int\> (0)**

  Last residue in helix

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team