NAME

       g_nmtraj - generate a virtual trajectory from an eigenvector

       VERSION 4.6.5

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 structure. 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 translational 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 (K)

       -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 2 Dec 2013                              g_nmtraj(1)