## Linux and UNIX Man Pages

Test Your Knowledge in Computers #953
Difficulty: Medium
A memory-resident virus installs itself as part of the operating system when executed, after which it remains in RAM from the time the computer is booted up to when it is shut down.
True or False?

# g_helixorient(1) [debian man page]

```g_helixorient(1)				 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				  g_helixorient(1)

NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
g_helixorient  -s  topol.tpr  -f traj.xtc -n index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise rise.xvg -oradius radius.xvg -otwist
twist.xvg -obending bending.xvg -otilt tilt.xvg -orot rotation.xvg -[no]h -[no]version -nice int  -b  time  -e  time  -dt  time	-xvg  enum
-[no]sidechain -[no]incremental

DESCRIPTION
g_helixorient	calculates  the coordinates and direction of the average axis inside an alpha helix, and the direction/vectors of both the
Calpha and (optionally) a sidechain atom relative to the axis.

As input, you need to specify an index group with Calpha atoms corresponding to an alpha-helix of continuous residues. Sidechain directions
require a second index group of the same size, containing the heavy atom in each residue that should represent the sidechain.

Note that this program does not do any fitting of structures.

We need four Calpha coordinates to define the local direction of the helix axis.

The  tilt/rotation  is  calculated from Euler rotations, where we define the helix axis as the local  x-axis, the residues/Calpha vector as
y, and the  z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we first tilt the	helix  axis  (1)  around  and  (2)
orthogonal  to  the  residues  vector, and finally apply the (3) rotation around it. For debugging or other purposes, we also write out the
actual Euler rotation angles as	theta[1-3].xvg

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

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

-n index.ndx Input, Opt.
Index file

-oaxis helixaxis.dat Output
Generic data file

-ocenter center.dat Output
Generic data file

-orise rise.xvg Output
xvgr/xmgr file

xvgr/xmgr file

-otwist twist.xvg Output
xvgr/xmgr file

-obending bending.xvg Output
xvgr/xmgr file

-otilt tilt.xvg Output
xvgr/xmgr file

-orot rotation.xvg Output
xvgr/xmgr file

OTHER OPTIONS
-[no]hno
Print help info and quit

-[no]versionno
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)

-xvg enum xmgrace
xvg plot formatting:  xmgrace,	xmgr or  none

-[no]sidechainno
Calculate sidechain directions relative to helix axis too.

-[no]incrementalno
Calculate incremental rather than total rotation/tilt.

gromacs(7)

Mon 4 Apr 2011						  g_helixorient(1)```

## Check Out this Related Man Page

```g_order(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_order(1)

NAME
g_order - computes the order parameter per atom for carbon tails

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
g_order	-f  traj.xtc  -n  index.ndx -nr index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -ob eiwit.pdb -os sliced.xvg -Sg sg-ang.xvg -Sk
sk-dist.xvg -Sgsl sg-ang-slice.xvg -Sksl sk-dist-slice.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d  enum
-sl int -[no]szonly -[no]unsat -[no]permolecule -[no]radial -[no]calcdist

DESCRIPTION
Compute the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis.  The index file should
contain only the groups to be used for calculations, with each group of equivalent carbons along the relevant acyl chain in its own  group.
There  should  not  be  any generic groups (like System, Protein) in the index file to avoid confusing the program (this is not relevant to
tetrahedral order parameters however, which only work for water anyway).

The program can also give all diagonal elements of the order tensor and even calculate the deuterium order parameter Scd (default). If  the
option	-szonly is given, only one order tensor component (specified by the  -d option) is given and the order parameter per slice is cal-
culated as well. If  -szonly is not selected, all diagonal elements and the deuterium order parameter is given.

The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters  are  calculated.	See  P.-L.
Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.  for more details.

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

-n index.ndx Input
Index file

-nr index.ndx Input
Index file

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

-o order.xvg Output
xvgr/xmgr file

-od deuter.xvg Output
xvgr/xmgr file

-ob eiwit.pdb Output
Protein data bank file

-os sliced.xvg Output
xvgr/xmgr file

-Sg sg-ang.xvg Output, Opt.
xvgr/xmgr file

-Sk sk-dist.xvg Output, Opt.
xvgr/xmgr file

-Sgsl sg-ang-slice.xvg Output, Opt.
xvgr/xmgr file

-Sksl sk-dist-slice.xvg Output, Opt.
xvgr/xmgr file

OTHER OPTIONS
-[no]hno
Print help info and quit

-[no]versionno
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)

-[no]wno
View output  .xvg,  .xpm,  .eps and  .pdb files

-xvg enum xmgrace
xvg plot formatting:  xmgrace,	xmgr or  none

-d enum z
Direction of the normal on the membrane:  z,  x or  y

-sl int 1
Calculate order parameter as function of box length, dividing the box in nr slices.

-[no]szonlyno
Only give Sz element of order tensor. (axis can be specified with  -d)

-[no]unsatno
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.

-[no]permoleculeno
Compute per-molecule Scd order parameters