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| GMX-NMENS(1) | GROMACS | GMX-NMENS(1) |
NAME
gmx-nmens - Generate an ensemble of structures from the normal modes
SYNOPSIS
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>]
DESCRIPTION
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
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
gmx(1)
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2025, GROMACS development team
| February 10, 2025 | 2025.0 |
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