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)