1 .TH g_rotmat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty"
3 g_rotmat - plots the rotation matrix for fitting to a reference structure
5 .B VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " rotmat.xvg "
13 .BI "\-[no]version" ""
25 \&g_rotmat plots the rotation matrix required for least squares fitting
26 \&a conformation onto the reference conformation provided with
27 \&\fB \-s\fR. Translation is removed before fitting.
28 \&The output are the three vectors that give the new directions
29 \&of the x, y and z directions of the reference conformation,
30 \&for example: (zx,zy,zz) is the orientation of the reference
31 \&z\-axis in the trajectory frame.
35 \&This tool is useful for, for instance,
36 \&determining the orientation of a molecule
37 \&at an interface, possibly on a trajectory produced with
38 \&\fB trjconv \-fit rotxy+transxy\fR to remove the rotation
43 \&Option \fB \-ref\fR determines a reference structure for fitting,
44 \&instead of using the structure from \fB \-s\fR. The structure with
45 \&the lowest sum of RMSD's to all other structures is used.
46 \&Since the computational cost of this procedure grows with
47 \&the square of the number of frames, the \fB \-skip\fR option
48 \&can be useful. A full fit or only a fit in the x/y plane can
53 \&Option \fB \-fitxy\fR fits in the x/y plane before determining
54 \&the rotation matrix.
58 Trajectory: xtc trr trj gro g96 pdb cpt
60 .BI "\-s" " topol.tpr"
62 Structure+mass(db): tpr tpb tpa gro g96 pdb
64 .BI "\-n" " index.ndx"
68 .BI "\-o" " rotmat.xvg"
74 Print help info and quit
76 .BI "\-[no]version" "no "
77 Print version info and quit
79 .BI "\-nice" " int" " 19"
82 .BI "\-b" " time" " 0 "
83 First frame (ps) to read from trajectory
85 .BI "\-e" " time" " 0 "
86 Last frame (ps) to read from trajectory
88 .BI "\-dt" " time" " 0 "
89 Only use frame when t MOD dt = first time (ps)
92 View output xvg, xpm, eps and pdb files
94 .BI "\-xvg" " enum" " xmgrace"
95 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
97 .BI "\-ref" " enum" " none"
98 Determine the optimal reference structure: \fB none\fR, \fB xyz\fR or \fB xy\fR
100 .BI "\-skip" " int" " 1"
101 Use every nr\-th frame for \-ref
103 .BI "\-[no]fitxy" "no "
104 Fit the x/y rotation before determining the rotation
106 .BI "\-[no]mw" "yes "
107 Use mass weighted fitting
112 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.