NAME
g_nmtraj - generate oscillating trajectory of an eigenmode
VERSION 4.0.1
SYNOPSIS
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
DESCRIPTION
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.
FILES
-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
OTHER OPTIONS
-[no]hno
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
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_nmtraj(1)