g_nmtraj_d (1) - Linux Manuals

g_nmtraj_d: generate oscillating trajectory of an eigenmode


g_nmtraj - generate oscillating trajectory of an eigenmode



g_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -nice int -eignr string -phases string -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 

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

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


 Print help info and quit

-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 in Kelvin

-amplitude real 0.25
 Amplitude for modes with eigenvalue=0

-nframes int 30
 Number of frames to generate



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