Man Linux: Main Page and Category List


       g_nmtraj - generate oscillating trajectory of an eigenmode

       VERSION 4.0.1


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


         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 unrealistic
       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.


       -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


        Print help 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



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                    g_nmtraj(1)