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 to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input)
-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
-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)
View output .xvg, .xpm, .eps and .pdb files
-r0 <int> (1)
The first residue number in the sequence
Check at every step which part of the sequence is helical
Toggle fit to a perfect helix
Print debug info
Write a new trajectory file for ED
-ahxstart <int> (0)
First residue in helix
-ahxend <int> (0)
Last residue in helix