1GMX-ROTMAT(1)                       GROMACS                      GMX-ROTMAT(1)
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NAME

6       gmx-rotmat - Plot the rotation matrix for fitting to a reference struc‐
7       ture
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SYNOPSIS

10          gmx rotmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
11                     [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
12                     [-[no]w] [-xvg <enum>] [-ref <enum>] [-skip <int>]
13                     [-[no]fitxy] [-[no]mw]
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DESCRIPTION

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

38       Options to specify input files:
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40       -f [<.xtc/.trr/…>] (traj.xtc)
41              Trajectory: xtc trr cpt gro g96 pdb tng
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43       -s [<.tpr/.gro/…>] (topol.tpr)
44              Structure+mass(db): tpr gro g96 pdb brk ent
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46       -n [<.ndx>] (index.ndx) (Optional)
47              Index file
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49       Options to specify output files:
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51       -o [<.xvg>] (rotmat.xvg)
52              xvgr/xmgr file
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54       Other options:
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56       -b <time> (0)
57              Time of first frame to read from trajectory (default unit ps)
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59       -e <time> (0)
60              Time of last frame to read from trajectory (default unit ps)
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62       -dt <time> (0)
63              Only use frame when t MOD dt = first time (default unit ps)
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65       -[no]w (no)
66              View output .xvg, .xpm, .eps and .pdb files
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68       -xvg <enum> (xmgrace)
69              xvg plot formatting: xmgrace, xmgr, none
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71       -ref <enum> (none)
72              Determine the optimal reference structure: none, xyz, xy
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74       -skip <int> (1)
75              Use every nr-th frame for -ref
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77       -[no]fitxy (no)
78              Fit the x/y rotation before determining the rotation
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80       -[no]mw (yes)
81              Use mass weighted fitting
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SEE ALSO

84       gmx(1)
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86       More     information    about    GROMACS    is    available    at    <‐
87       http://www.gromacs.org/>.
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90       2019, GROMACS development team
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952018.7                           May 29, 2019                    GMX-ROTMAT(1)
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