g_rotmat(1) - Linux man page

Name

g_rotmat - plots the rotation matrix for fitting to a reference structure

VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

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

Description

g_rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided with -s. Translation is removed before fitting. The output are the three vectors that give the new directions of the x, y and z directions of the reference conformation, for example: (zx,zy,zz) is the orientation of the reference z-axis in the trajectory frame.

This tool is useful for, for instance, determining the orientation of a molecule at an interface, possibly on a trajectory produced with trjconv -fit rotxy+transxy to remove the rotation in the x-y plane.

Option -ref determines a reference structure for fitting, instead of using the structure from -s. The structure with the lowest sum of RMSD's to all other structures is used. Since the computational cost of this procedure grows with the square of the number of frames, the -skip option can be useful. A full fit or only a fit in the x-y plane can be performed.

Option -fitxy fits in the x-y plane before determining the rotation matrix.

Files

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

-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb

-n index.ndx Input, Opt. Index file

-o rotmat.xvg Output xvgr/xmgr file

Other Options

-[no]hno Print help info and quit

-[no]versionno Print version 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

-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none

-ref enum none Determine the optimal reference structure: none, xyz or xy

-skip int 1 Use every nr-th frame for -ref

-[no]fitxyno Fit the x/y rotation before determining the rotation