g_nmtraj(1)
NAME
g_nmtraj - generate a virtual trajectory from an eigenvector
SYNOPSIS
g_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -[no]X -nice int -eignr int -temp real -amplitude real -nframes int
DESCRIPTION
g_nmtraj generates a 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(1)
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.
OPTIONS
- -s topol.tpr
- Structure+mass(db) (Input): tpr tpb tpa gro g96 pdb xml
- -v eigenvec.trr
- Full precision trajectory (Input): trr trj
- -o nmtraj.xtc
- Generic trajectory (Output): xtc trr trj gro g96 pdb
- -[no]h Print help info and quit (default: no).
- -[no]X Use dialog box GUI to edit command line options (default: no).
- -nice int
- Set the nicelevel (default: 19).
- -eignr int
- Eigenvector to use (default: 7). The first is 1.
- -temp real
- Temperature, in Kelvin (default: 300).
- -amplitude real
- Amplitude for modes with eigenvalue <= 0 (default: 0.25).
- -nframes int
- Number of frames to generate (default: 30).
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at http://www.gromacs.org/.