1GMX-HELIX(1)                        GROMACS                       GMX-HELIX(1)
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NAME

6       gmx-helix - Calculate basic properties of alpha helices
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SYNOPSIS

9          gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
10                    [-cz [<.gro/.g96/...>]] [-b <time>] [-e <time>]
11                    [-dt <time>] [-[no]w] [-r0 <int>] [-[no]q] [-[no]F]
12                    [-[no]db] [-[no]ev] [-ahxstart <int>] [-ahxend <int>]
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DESCRIPTION

15       gmx helix computes all kinds of helix properties. First, the peptide is
16       checked to find the longest helical part,  as  determined  by  hydrogen
17       bonds  and phi/psi angles.  That bit is fitted to an ideal helix around
18       the z-axis and centered around the origin.  Then the following  proper‐
19       ties are computed:
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21          • Helix  radius  (file radius.xvg). This is merely the RMS deviation
22            in two dimensions for all  Calpha  atoms.   it  is  calculated  as
23            sqrt((sum_i  (x^2(i)+y^2(i)))/N) where N is the number of backbone
24            atoms. For an ideal helix the radius is 0.23 nm.
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26          • Twist (file twist.xvg). The average helical angle per  residue  is
27            calculated. For an alpha-helix it is 100 degrees, for 3-10 helices
28            it will be smaller, and for 5-helices it will be larger.
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30          • Rise per residue (file rise.xvg). The helical rise per residue  is
31            plotted  as  the  difference in z-coordinate between Calpha atoms.
32            For an ideal helix, this is 0.15 nm.
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34          • Total helix length (file len-ahx.xvg). The total length of the he‐
35            lix  in  nm. This is simply the average rise (see above) times the
36            number of helical residues (see below).
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38          • Helix dipole, backbone only (file dip-ahx.xvg).
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40          • RMS deviation from ideal helix, calculated for  the  Calpha  atoms
41            only (file rms-ahx.xvg).
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43          • Average Calpha - Calpha dihedral angle (file phi-ahx.xvg).
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45          • Average phi and psi angles (file phipsi.xvg).
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47          • Ellipticity at 222 nm according to Hirst and Brooks.
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OPTIONS

50       Options to specify input files:
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52       -s [<.tpr>] (topol.tpr)
53              Portable xdr run input file
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55       -n [<.ndx>] (index.ndx)
56              Index file
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58       -f [<.xtc/.trr/...>] (traj.xtc)
59              Trajectory: xtc trr cpt gro g96 pdb tng
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61       Options to specify output files:
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63       -cz [<.gro/.g96/...>] (zconf.gro)
64              Structure file: gro g96 pdb brk ent esp
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66       Other options:
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68       -b <time> (0)
69              Time of first frame to read from trajectory (default unit ps)
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71       -e <time> (0)
72              Time of last frame to read from trajectory (default unit ps)
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74       -dt <time> (0)
75              Only use frame when t MOD dt = first time (default unit ps)
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77       -[no]w (no)
78              View output .xvg, .xpm, .eps and .pdb files
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80       -r0 <int> (1)
81              The first residue number in the sequence
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83       -[no]q (no)
84              Check at every step which part of the sequence is helical
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86       -[no]F (yes)
87              Toggle fit to a perfect helix
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89       -[no]db (no)
90              Print debug info
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92       -[no]ev (no)
93              Write a new 'trajectory' file for ED
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95       -ahxstart <int> (0)
96              First residue in helix
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98       -ahxend <int> (0)
99              Last residue in helix
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SEE ALSO

102       gmx(1)
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104       More     information    about    GROMACS    is    available    at    <‐
105       http://www.gromacs.org/>.
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108       2022, GROMACS development team
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1132022.2                           Jun 16, 2022                     GMX-HELIX(1)
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