gmx-nmtraj(1) GROMACS Manual gmx-nmtraj(1)NAMEgmx-nmtraj - Generate a virtual oscillating trajectory from an eigen‐
vector
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, corre‐
sponding to a harmonic Cartesian oscillation around the average struc‐
ture. The eigenvectors should normally be mass-weighted, but you can
use non-weighted eigenvectors to generate orthogonal motions. The out‐
put frames are written as a trajectory file covering an entire period,
and the first frame is the average structure. If you write the trajec‐
tory in (or convert to) PDB format you can view it directly in PyMol
and also render a photorealistic movie. Motion amplitudes are calcu‐
lated from the eigenvalues and a preset temperature, assuming equipar‐
tition 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 dis‐
placements and mass weighting will lead to serious structure deforma‐
tion for high amplitudes - this is is simply a limitation of the Carte‐
sian normal mode model. By default the selected eigenvector is set to
7, since the first six normal modes are the translational and rota‐
tional 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-nmtraj(1)