1g_sgangle(1)              GROMACS suite, VERSION 4.5              g_sgangle(1)
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NAME

6       g_sgangle - computes the angle and distance between two groups
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8       VERSION 4.5
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SYNOPSIS

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

16       Compute  the  angle  and  distance  between two groups.  The groups are
17       defined by a number of atoms given in an index file and may be  two  or
18       three  atoms  in size.  If -one is set, only one group should be speci‐
19       fied in the index file and the angle between this group at time 0 and t
20       will  be  computed.  The angles calculated depend on the order in which
21       the atoms are given. Giving for instance 5 6 will rotate the vector 5-6
22       with 180 degrees compared to giving 6 5.
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24       If  three  atoms  are  given,  the normal on the plane spanned by those
25       three atoms will be calculated, using the formula  P1P2  x  P1P3.   The
26       cos  of the angle is calculated, using the inproduct of the two normal‐
27       ized vectors.
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30       Here is what some of the file options do:
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32       -oa: Angle between the two groups specified in the  index  file.  If  a
33       group  contains  three  atoms  the normal to the plane defined by those
34       three atoms will be used. If a group contains  two  atoms,  the  vector
35       defined by those two atoms will be used.
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37       -od:  Distance between two groups. Distance is taken from the center of
38       one group to the center of the other group.
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40       -od1: If one plane and one vector is given, the distances for  each  of
41       the atoms from the center of the plane is given separately.
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43       -od2: For two planes this option has no meaning.
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FILES

46       -f traj.xtc Input
47        Trajectory: xtc trr trj gro g96 pdb cpt
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49       -n index.ndx Input
50        Index file
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52       -s topol.tpr Input
53        Run input file: tpr tpb tpa
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55       -oa sg_angle.xvg Output
56        xvgr/xmgr file
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58       -od sg_dist.xvg Output, Opt.
59        xvgr/xmgr file
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61       -od1 sg_dist1.xvg Output, Opt.
62        xvgr/xmgr file
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64       -od2 sg_dist2.xvg Output, Opt.
65        xvgr/xmgr file
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OTHER OPTIONS

69       -[no]hno
70        Print help info and quit
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72       -[no]versionno
73        Print version info and quit
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75       -nice int 19
76        Set the nicelevel
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78       -b time 0
79        First frame (ps) to read from trajectory
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81       -e time 0
82        Last frame (ps) to read from trajectory
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84       -dt time 0
85        Only use frame when t MOD dt = first time (ps)
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87       -[no]wno
88        View output xvg, xpm, eps and pdb files
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90       -xvg enum xmgrace
91        xvg plot formatting:  xmgrace,  xmgr or  none
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93       -[no]oneno
94        Only one group compute angle between vector at time zero and time t
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96       -[no]zno
97        Use the Z-axis as reference
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SEE ALSO

101       gromacs(7)
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103       More   information  about  GROMACS  is  available  at  <http://www.gro‐
104       macs.org/>.
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108                                Thu 26 Aug 2010                   g_sgangle(1)