Provided by: gromacs-data_2019.3-2_all

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

```

SEEALSO

```       gmx(1)

```       2019, GROMACS development team