1g_nmtraj(1)               GROMACS suite, VERSION 4.5               g_nmtraj(1)
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NAME

6       g_nmtraj - generate a virtual trajectory from an eigenvector
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8       VERSION 4.5
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SYNOPSIS

11       g_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -[no]version
12       -nice int -eignr string  -phases  string  -temp  real  -amplitude  real
13       -nframes int
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DESCRIPTION

16         g_nmtraj  generates an virtual trajectory from an eigenvector, corre‐
17       sponding to a harmonic cartesian oscillation around the average  struc‐
18       ture.  The  eigenvectors  should normally be mass-weighted, but you can
19       use non-weighted eigenvectors to generate orthogonal motions.  The out‐
20       put  frames are written as a trajectory file covering an entire period,
21       and the first frame is the average structure. If you write the  trajec‐
22       tory  in  (or  convert to) PDB format you can view it directly in PyMol
23       and also render a photorealistic movie.  Motion amplitudes  are  calcu‐
24       lated  from the eigenvalues and a preset temperature, assuming equipar‐
25       tition of the energy over all modes. To make the motion clearly visible
26       in  PyMol  you  might want to amplify it by setting an unrealistic high
27       temperature.  However, be aware that both  the  linear  cartesian  dis‐
28       placements  and  mass weighting will lead to serious structure deforma‐
29       tion for high amplitudes - this is is simply a limitation of the carte‐
30       sian  normal  mode model. By default the selected eigenvector is set to
31       7, since  the first six normal modes are the  translational  and  rota‐
32       tional degrees of freedom.
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FILES

35       -s topol.tpr Input
36        Structure+mass(db): tpr tpb tpa gro g96 pdb
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38       -v eigenvec.trr Input
39        Full precision trajectory: trr trj cpt
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41       -o nmtraj.xtc Output
42        Trajectory: xtc trr trj gro g96 pdb
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OTHER OPTIONS

46       -[no]hno
47        Print help info and quit
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49       -[no]versionno
50        Print version info and quit
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52       -nice int 19
53        Set the nicelevel
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55       -eignr string 7
56        String of eigenvectors to use (first is 1)
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58       -phases string 0.0
59        String of phases (default is 0.0)
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61       -temp real 300
62        Temperature in Kelvin
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64       -amplitude real 0.25
65        Amplitude for modes with eigenvalue=0
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67       -nframes int 30
68        Number of frames to generate
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SEE ALSO

72       gromacs(7)
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74       More   information  about  GROMACS  is  available  at  <http://www.gro‐
75       macs.org/>.
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79                                Thu 26 Aug 2010                    g_nmtraj(1)
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