1 .TH g_nmtraj 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_nmtraj - generate a virtual trajectory from an eigenvector
8 .BI "\-s" " topol.tpr "
9 .BI "\-v" " eigenvec.trr "
10 .BI "\-o" " nmtraj.xtc "
12 .BI "\-[no]version" ""
14 .BI "\-eignr" " string "
15 .BI "\-phases" " string "
17 .BI "\-amplitude" " real "
18 .BI "\-nframes" " int "
20 \&\fB g_nmtraj\fR generates an virtual trajectory from an eigenvector,
21 \&corresponding to a harmonic cartesian oscillation around the average
22 \&structure. The eigenvectors should normally be mass\-weighted, but you can
23 \&use non\-weighted eigenvectors to generate orthogonal motions.
24 \&The output frames are written as a trajectory file covering an entire period, and
25 \&the first frame is the average structure. If you write the trajectory in (or convert to)
26 \&PDB format you can view it directly in PyMol and also render a photorealistic movie.
27 \&Motion amplitudes are calculated from the eigenvalues and a preset temperature,
28 \&assuming equipartition of the energy over all modes. To make the motion clearly visible
29 \&in PyMol you might want to amplify it by setting an unrealistic high temperature.
30 \&However, be aware that both the linear cartesian displacements and mass weighting will
31 \&lead to serious structure deformation for high amplitudes \- this is is simply a limitation
32 \&of the cartesian normal mode model. By default the selected eigenvector is set to 7, since
33 \& the first six normal modes are the translational and rotational degrees of freedom.
35 .BI "\-s" " topol.tpr"
37 Structure+mass(db): tpr tpb tpa gro g96 pdb
39 .BI "\-v" " eigenvec.trr"
41 Full precision trajectory: trr trj cpt
43 .BI "\-o" " nmtraj.xtc"
45 Trajectory: xtc trr trj gro g96 pdb
49 Print help info and quit
51 .BI "\-[no]version" "no "
52 Print version info and quit
54 .BI "\-nice" " int" " 19"
57 .BI "\-eignr" " string" " 7"
58 String of eigenvectors to use (first is 1)
60 .BI "\-phases" " string" " 0.0"
61 String of phases (default is 0.0)
63 .BI "\-temp" " real" " 300 "
66 .BI "\-amplitude" " real" " 0.25 "
67 Amplitude for modes with eigenvalue=0
69 .BI "\-nframes" " int" " 30"
70 Number of frames to generate
75 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.