This is the command gmx-nmtraj that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-nmtraj - Generate a virtual oscillating trajectory from an eigenvector
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, corresponding to a
harmonic Cartesian oscillation around the average structure. The eigenvectors should
normally be mass-weighted, but you can use non-weighted eigenvectors to generate
orthogonal motions. The output frames are written as a trajectory file covering an entire
period, and the first frame is the average structure. If you write the trajectory in (or
convert to) PDB format you can view it directly in PyMol and also render a photorealistic
movie. Motion amplitudes are calculated from the eigenvalues and a preset temperature,
assuming equipartition 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 deformation 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 rotational degrees of freedom.
OPTIONS
Options to specify input files:
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-v [<.trr/.cpt/...>] (eigenvec.trr)
Full precision trajectory: trr cpt tng
Options to specify output files:
-o [<.xtc/.trr/...>] (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
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