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

# g\_helix\_d(1)

Calculate basic properties of alpha helices

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

## NAME

gmx-helix - Calculate basic properties of alpha helices

## SYNOPSIS

gmx helix \[-s \[\<.tpr/.tpb/...\>\]\] \[-n \[\<.ndx\>\]\]\
           \[-f \[\<.xtc/.trr/...\>\]\] \[-cz \[\<.gro/.g96/...\>\]\]\
           \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\] \[-\[no\]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:

**1.** 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 (x2(i)+y2(i)))/N) where N is the number of backbone atoms. For an ideal helix the radius is 0.23 nm **2.** 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. **3.** 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 **4.** 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). **5.** Helix dipole, backbone only (file **dip-ahx.xvg**). **6.** RMS deviation from ideal helix, calculated for the Calpha atoms only (file **rms-ahx.xvg**). **7.** Average Calpha - Calpha dihedral angle (file **phi-ahx.xvg**). **8.** Average phi and psi angles (file **phipsi.xvg**). **9.** Ellipticity at 222 nm according to Hirst and Brooks.

## OPTIONS

Options to specify input and output files:

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Run input file: tpr tpb tpa

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

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-cz** *\[\<.gro/.g96/...\>\] (zconf.gro) (Output)*\
     Structure file: gro g96 pdb brk ent esp

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-b** *\<time\> (0)*\
     First frame (ps) to read from trajectory

**-e** *\<time\> (0)*\
     Last frame (ps) to read from trajectory

**-dt** *\<time\> (0)*\
     Only use frame when t MOD dt = first time (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

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

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