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NAME

       gmx-nmtraj - Generate a virtual oscillating trajectory from an eigenvector

SYNOPSIS

          gmx nmtraj [-s [<.tpr/.gro/...>]] [-v [<.trr/.cpt/...>]]
                     [-o [<.xtc/.trr/...>]] [-eignr <string>]
                     [-phases <string>] [-temp <real>] [-amplitude <real>]
                     [-nframes <int>]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -s [<.tpr/.gro/…>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -v [<.trr/.cpt/…>] (eigenvec.trr)
              Full precision trajectory: trr cpt tng

       Options to specify output files:

       -o [<.xtc/.trr/…>] (nmtraj.xtc)
              Trajectory: xtc trr gro g96 pdb tng

       Other options:

       -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

       gmx(1)

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

COPYRIGHT

       2019, GROMACS development team