Man Linux: Main Page and Category List

## NAME

```       g_sgangle - computes the angle and distance between two groups

VERSION 4.0.1

```

## SYNOPSIS

```       g_sgangle  -f  traj.xtc  -n index.ndx -s topol.tpr -oa sg_angle.xvg -od
sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg  -[no]h  -nice  int  -b
time -e time -dt time -[no]w -[no]xvgr -[no]one -[no]z

```

## DESCRIPTION

```       Compute  the  angle  and  distance  between two groups.  The groups are
defined by a number of atoms given in an index file and may be  two  or
three  atoms  in  size.   If  -one  is  set,  only  one group should be
specified in the index file and the angle between this group at time  0
and  t  will be computed.  The angles calculated depend on the order in
which the atoms are given. Giving for instance  5  6  will  rotate  the
vector 5-6 with 180 degrees compared to giving 6 5.

If  three  atoms  are  given,  the normal on the plane spanned by those
three atoms will be calculated, using the formula  P1P2  x  P1P3.   The
cos  of  the  angle  is  calculated,  using  the  inproduct  of the two
normalized vectors.

Here is what some of the file options do:

-oa: Angle between the two groups specified in the  index  file.  If  a
group  contains  three  atoms  the normal to the plane defined by those
three atoms will be used. If a group contains  two  atoms,  the  vector
defined by those two atoms will be used.

-od:  Distance between two groups. Distance is taken from the center of
one group to the center of the other group.

-od1: If one plane and one vector is given, the distances for  each  of
the atoms from the center of the plane is given seperately.

-od2: For two planes this option has no meaning.

```

## FILES

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

-n index.ndx Input
Index file

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

-oa sg_angle.xvg Output
xvgr/xmgr file

-od sg_dist.xvg Output, Opt.
xvgr/xmgr file

-od1 sg_dist1.xvg Output, Opt.
xvgr/xmgr file

-od2 sg_dist2.xvg Output, Opt.
xvgr/xmgr file

```

## OTHEROPTIONS

```       -[no]hno
Print help 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

-[no]xvgryes
Add  specific  codes  (legends  etc.)  in the output xvg files for the
xmgrace program

-[no]oneno
Only one group compute angle between vector at time zero and time t

-[no]zno
Use the Z-axis as reference

```

```       gromacs(7)