1GMX-NMTRAJ(1) GROMACS GMX-NMTRAJ(1)
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6 gmx-nmtraj - Generate a virtual oscillating trajectory from an eigen‐
7 vector
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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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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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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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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 2020, GROMACS development team
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772019.6 Feb 28, 2020 GMX-NMTRAJ(1)