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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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