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

6       gmx-nmtraj  -  Generate a virtual oscillating trajectory from an eigen‐
7       vector
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SYNOPSIS

10          gmx nmtraj [-s [<.tpr/.gro/...>]] [-v [<.trr/.cpt/...>]]
11                     [-o [<.xtc/.trr/...>]] [-eignr <string>]
12                     [-phases <string>] [-temp <real>] [-amplitude <real>]
13                     [-nframes <int>]
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DESCRIPTION

16       gmx 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  unrealistically
27       high  temperature.   However,  be  aware that both the linear Cartesian
28       displacements and mass weighting will lead to serious structure  defor‐
29       mation  for  high  amplitudes  -  this is is simply a limitation of the
30       Cartesian normal mode model. By default the selected eigenvector is set
31       to  7, since the first six normal modes are the translational and rota‐
32       tional degrees of freedom.
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OPTIONS

35       Options to specify input files:
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37       -s [<.tpr/.gro/...>] (topol.tpr)
38              Structure+mass(db): tpr gro g96 pdb brk ent
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40       -v [<.trr/.cpt/...>] (eigenvec.trr)
41              Full precision trajectory: trr cpt tng
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43       Options to specify output files:
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45       -o [<.xtc/.trr/...>] (nmtraj.xtc)
46              Trajectory: xtc trr gro g96 pdb tng
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48       Other options:
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50       -eignr <string> (7)
51              String of eigenvectors to use (first is 1)
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53       -phases <string> (0.0)
54              String of phases (default is 0.0)
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56       -temp <real> (300)
57              Temperature (K)
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59       -amplitude <real> (0.25)
60              Amplitude for modes with eigenvalue<=0
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62       -nframes <int> (30)
63              Number of frames to generate
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SEE ALSO

66       gmx(1)
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68       More    information    about    GROMACS    is    available    at     <‐
69       http://www.gromacs.org/>.
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72       2022, GROMACS development team
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772022.3                           Sep 02, 2022                    GMX-NMTRAJ(1)
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