1g_roGtRmOaMtA(C1S)suite, VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7bga_-rdoitrmtayt(1)
2
3
4

NAME

6       g_rotmat  - plots the rotation matrix for fitting to a reference struc‐
7       ture
8
9       VERSION 4.5-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty
10

SYNOPSIS

12       g_rotmat -f traj.xtc -s topol.tpr -n  index.ndx  -o  rotmat.xvg  -[no]h
13       -[no]version  -nice  int -b time -e time -dt time -[no]w -xvg enum -ref
14       enum -skip int -[no]fitxy -[no]mw
15

DESCRIPTION

17       g_rotmat plots the rotation matrix required for least squares fitting a
18       conformation  onto the reference conformation provided with  -s. Trans‐
19       lation is removed before fitting.  The output  are  the  three  vectors
20       that give the new directions of the x, y and z directions of the refer‐
21       ence conformation, for example: (zx,zy,zz) is the  orientation  of  the
22       reference z-axis in the trajectory frame.
23
24
25       This tool is useful for, for instance, determining the orientation of a
26       molecule at an interface, possibly on a trajectory produced with   trj‐
27       conv -fit rotxy+transxy to remove the rotation in the xy-plane.
28
29
30       Option   -ref  determines a reference structure for fitting, instead of
31       using the structure from  -s. The structure  with  the  lowest  sum  of
32       RMSD's  to  all other structures is used.  Since the computational cost
33       of this procedure grows with the square of the number  of  frames,  the
34       -skip  option  can be useful. A full fit or only a fit in the x/y plane
35       can be performed.
36
37
38       Option  -fitxy fits in the x/y plane before  determining  the  rotation
39       matrix.
40

FILES

42       -f traj.xtc Input
43        Trajectory: xtc trr trj gro g96 pdb cpt
44
45       -s topol.tpr Input
46        Structure+mass(db): tpr tpb tpa gro g96 pdb
47
48       -n index.ndx Input, Opt.
49        Index file
50
51       -o rotmat.xvg Output
52        xvgr/xmgr file
53
54

OTHER OPTIONS

56       -[no]hno
57        Print help info and quit
58
59       -[no]versionno
60        Print version info and quit
61
62       -nice int 19
63        Set the nicelevel
64
65       -b time 0
66        First frame (ps) to read from trajectory
67
68       -e time 0
69        Last frame (ps) to read from trajectory
70
71       -dt time 0
72        Only use frame when t MOD dt = first time (ps)
73
74       -[no]wno
75        View output xvg, xpm, eps and pdb files
76
77       -xvg enum xmgrace
78        xvg plot formatting:  xmgrace,  xmgr or  none
79
80       -ref enum none
81        Determine the optimal reference structure:  none,  xyz or  xy
82
83       -skip int 1
84        Use every nr-th frame for -ref
85
86       -[no]fitxyno
87        Fit the x/y rotation before determining the rotation
88
89       -[no]mwyes
90        Use mass weighted fitting
91
92

SEE ALSO

94       gromacs(7)
95
96       More   information  about  GROMACS  is  available  at  <http://www.gro‐
97       macs.org/>.
98
99
100
101                                Thu 26 Aug 2010                    g_rotmat(1)
Impressum