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gmx-nmtraj(1)                   GROMACS Manual                   gmx-nmtraj(1)

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

SYNOPSIS
       gmx nmtraj [-s [<.tpr/.tpb/...>]] [-v [<.trr/.cpt/...>]]
                  [-o [<.xtc/.trr/...>]] [-nice <int>] [-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 and output files:

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

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

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

       Other options:

       -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/>.

VERSION 5.0.6                                                    gmx-nmtraj(1)