.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_helix - calculates basic properties of alpha helices

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_helix\fP
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-f" " traj.xtc "
.BI "\-to" " gtraj.g87 "
.BI "\-cz" " zconf.gro "
.BI "\-co" " waver.gro "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-r0" " int "
.BI "\-[no]q" ""
.BI "\-[no]F" ""
.BI "\-[no]db" ""
.BI "\-prop" " enum "
.BI "\-[no]ev" ""
.BI "\-ahxstart" " int "
.BI "\-ahxend" " int "
.SH DESCRIPTION
\&\fB g_helix\fR 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 \fI z\fR\-axis and centered around the origin.
\&Then the following properties are computed:


\&\fB 1.\fR Helix radius (file \fB radius.xvg\fR). This is merely the
\&RMS deviation in two dimensions for all Calpha atoms.
\&it is calced 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

\&\fB 2.\fR Twist (file \fB twist.xvg\fR). 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.

\&\fB 3.\fR Rise per residue (file \fB rise.xvg\fR). The helical rise per
\&residue is plotted as the difference in \fI z\fR\-coordinate between Calpha
\&atoms. For an ideal helix, this is 0.15 nm

\&\fB 4.\fR Total helix length (file \fB len\-ahx.xvg\fR). The total length
\&of the
\&helix in nm. This is simply the average rise (see above) times the
\&number of helical residues (see below).

\&\fB 5.\fR Number of helical residues (file \fB n\-ahx.xvg\fR). The title says
\&it all.

\&\fB 6.\fR Helix dipole, backbone only (file \fB dip\-ahx.xvg\fR).

\&\fB 7.\fR RMS deviation from ideal helix, calculated for the Calpha
\&atoms only (file \fB rms\-ahx.xvg\fR).

\&\fB 8.\fR Average Calpha \- Calpha dihedral angle (file \fB phi\-ahx.xvg\fR).

\&\fB 9.\fR Average phi and psi angles (file \fB phipsi.xvg\fR).

\&\fB 10.\fR Ellipticity at 222 nm according to Hirst and Brooks.
\&


.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-to" " gtraj.g87" 
.B Output, Opt.
 Gromos\-87 ASCII trajectory format 

.BI "\-cz" " zconf.gro" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-co" " waver.gro" 
.B Output
 Structure file: gro g96 pdb etc. 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-r0"  " int" " 1" 
 The first residue number in the sequence

.BI "\-[no]q"  "no    "
 Check at every step which part of the sequence is helical

.BI "\-[no]F"  "yes   "
 Toggle fit to a perfect helix

.BI "\-[no]db"  "no    "
 Print debug info

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

.BI "\-[no]ev"  "no    "
 Write a new 'trajectory' file for ED

.BI "\-ahxstart"  " int" " 0" 
 First residue in helix

.BI "\-ahxend"  " int" " 0" 
 Last residue in helix

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.