g_nmtraj(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_nmtraj(1)

NAME

       g_nmtraj - generate a virtual trajectory from an eigenvector

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_nmtraj  -s  topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -[no]version -nice int -eignr string -phases string -temp real -amplitude real
       -nframes int

DESCRIPTION

	g_nmtraj generates an virtual trajectory from an eigenvector, corresponding to a harmonic Cartesian oscillation around the average  struc-
       ture.  The  eigenvectors  should  normally be mass-weighted, but you can use non-weighted eigenvectors to generate orthogonal motions.  The
       output frames are written as a trajectory file covering an entire period, and the first frame is the average structure. If  you	write  the
       trajectory  in  (or convert to) PDB format you can view it directly in PyMol and also render a photorealistic movie.  Motion amplitudes are
       calculated from the eigenvalues and a preset temperature, assuming equipartition of the energy over all modes. To make the  motion  clearly
       visible	in  PyMol  you	might  want  to amplify it by setting an unrealistically high temperature.  However, be aware that both the linear
       Cartesian displacements and mass weighting will lead to serious structure deformation for high amplitudes - this is is simply a	limitation
       of  the	Cartesian  normal  mode model. By default the selected eigenvector is set to 7, since  the first six normal modes are the transla-
       tional and rotational degrees of freedom.

FILES

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

       -v eigenvec.trr Input
	Full precision trajectory: trr trj cpt

       -o nmtraj.xtc Output
	Trajectory: xtc trr trj gro g96 pdb

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -eignr string 7
	String of eigenvectors to use (first is 1)

       -phases string 0.0
	String of phases (default is 0.0)

       -temp real 300
	Temperature in Kelvin

       -amplitude real 0.25
	Amplitude for modes with eigenvalue=0

       -nframes int 30
	Number of frames to generate

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_nmtraj(1)