Provided by: gromacs-data_4.6.5-1build1_all bug


       g_helix - calculates basic properties of alpha helices

       VERSION 4.6.5


       g_helix  -s  topol.tpr  -n index.ndx -f traj.xtc -to gtraj.g87 -cz zconf.gro -co waver.gro
       -[no]h -[no]version -nice int -b time -e time  -dt  time  -[no]w  -r0  int  -[no]q  -[no]F
       -[no]db -prop enum -[no]ev -ahxstart int -ahxend int


        g_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

        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.


       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input
        Index file

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -to gtraj.g87 Output, Opt.
        Gromos-87 ASCII trajectory format

       -cz zconf.gro Output
        Structure file: gro g96 pdb etc.

       -co waver.gro Output
        Structure file: gro g96 pdb etc.


        Print help info and quit

        Print version info and quit

       -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

       -prop enum RAD
        Select  property  to  weight eigenvectors with. WARNING experimental stuff:  RAD,  TWIST,
       RISE,  LEN,  NHX,  DIP,  RMS,  CPHI,  RMSA,  PHI,  PSI,  HB3,  HB4,  HB5 or  CD222

        Write a new 'trajectory' file for ED

       -ahxstart int 0
        First residue in helix

       -ahxend int 0
        Last residue in helix



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               g_helix(1)