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)
              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

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team