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gmx-nmtraj(1)			GROMACS Manual			 gmx-nmtraj(1)

NAME
       gmx-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 ALSO
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							 gmx-nmtraj(1)

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