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GMX-NMTRAJ(1)			    GROMACS			 GMX-NMTRAJ(1)

NAME
       gmx-nmtraj  -  Generate a virtual oscillating trajectory	from an	eigen-
       vector

SYNOPSIS
	  gmx nmtraj [-s [_.tpr/.gro/..._]] [-v	[_.trr/.cpt/..._]]
		     [-o [_.xtc/.trr/..._]] [-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
       displacements and mass weighting	will lead to serious structure	defor-
       mation  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 rota-
       tional degrees of freedom.

OPTIONS
       Options to specify input	files:

       -s [<.tpr/.gro/^a|>] (topol.tpr)
	      Structure+mass(db): tpr gro g96 pdb brk ent

       -v [<.trr/.cpt/^a|>] (eigenvec.trr)
	      Full precision trajectory: trr cpt tng

       Options to specify output files:

       -o [<.xtc/.trr/^a|>] (nmtraj.xtc)
	      Trajectory: xtc trr gro g96 pdb tng

       Other options:

       -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
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020			 GMX-NMTRAJ(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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