g_nmtraj VERSION 3.3

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

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 xml

-v eigenvec.trr Input Full precision trajectory: trr trj

-o nmtraj.xtc Output Generic trajectory: xtc trr trj gro g96 pdb

-[no]h no Print help info and quit

-[no]X no Use dialog box GUI to edit command line options

-nice int 19 Set the nicelevel

-eignr int 7 Eigenvector to use (first is 1)

-temp real 300 Temperature, in Kelvin

-amplitude real 0.25 Amplitude for modes with eigenvalue <= 0

-nframes int 30 Number of frames to generate

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.