table of contents
g_rotmat(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_rotmat(1) |
NAME¶
g_rotmat - plots the rotation matrix for fitting to a reference structureSYNOPSIS¶
g_rotmat -f traj.xtc -s topol.tpr -n index.ndx -o rotmat.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ref enum -skip int -[no]fitxy -[no]mwDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Determine the optimal reference structure: none, xyz or xy
Use every nr-th frame for -ref
Fit the x/y rotation before determining the rotation
Use mass weighted fitting
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |