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GMX-NMENS(1) GROMACS GMX-NMENS(1)

gmx-nmens - Generate an ensemble of structures from the normal modes

gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]


          [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]


          [-temp <real>] [-seed <int>] [-num <int>] [-first <int>]


          [-last <int>]


gmx nmens generates an ensemble around an average structure in a subspace that is defined by a set of normal modes (eigenvectors). The eigenvectors are assumed to be mass-weighted. The position along each eigenvector is randomly taken from a Gaussian distribution with variance kT/eigenvalue.

By default the starting eigenvector is set to 7, since the first six normal modes are the translational and rotational degrees of freedom.

Options to specify input files:

Full precision trajectory: trr cpt tng
xvgr/xmgr file
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

Trajectory: xtc trr gro g96 pdb tng

Other options:

xvg plot formatting: xmgrace, xmgr, none
Temperature in Kelvin
Random seed (0 means generate)
Number of structures to generate
First eigenvector to use (-1 is select)
Last eigenvector to use (-1 is till the last)

gmx(1)

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2023, GROMACS development team

February 3, 2023 2022.5