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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                     GMX-NMTRAJ(1)

gmxnmtraj  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.

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

       Options to specify input files:

       -s[<.tpr/.gro/...>](topol.tpr)
              Structure+mass(db): tprgrog96pdb brk ent

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

       Options to specify output files:

       -o[<.xtc/.trr/...>](nmtraj.xtc)
              Trajectory: xtctrrgrog96pdbtng

       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

gmx(1)

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

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