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gmx-nmens - Man Page

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:

-v [<.trr/.cpt/...>] (eigenvec.trr)

Full precision trajectory: trr cpt tng

-e [<.xvg>] (eigenval.xvg)

xvgr/xmgr file

-s [<.tpr/.gro/...>] (topol.tpr)

Structure+mass(db): tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-o [<.xtc/.trr/...>] (ensemble.xtc)

Trajectory: xtc trr gro g96 pdb tng

Other options:

-xvg <enum> (xmgrace)

xvg plot formatting: xmgrace, xmgr, none

-temp <real> (300)

Temperature in Kelvin

-seed <int> (0)

Random seed (0 means generate)

-num <int> (100)

Number of structures to generate

-first <int> (7)

First eigenvector to use (-1 is select)

-last <int> (-1)

Last eigenvector to use (-1 is till the last)

See Also


More information about GROMACS is available at <http://www.gromacs.org/>.

Referenced By


Feb 28, 2024 2024.1 GROMACS