Man page - gmx-nmens(1)
Packages contas this manual
- gmx-wham(1)
- gmx-trjcat(1)
- gmx-confrms(1)
- gmx_d(1)
- gmx-xpm2ps(1)
- gmx-make_edi(1)
- gmx-solvate(1)
- gmx-awh(1)
- gmx-help(1)
- gmx-hydorder(1)
- gmx-velacc(1)
- gmx-order(1)
- gmx-clustsize(1)
- gmx-densorder(1)
- gmx-msd(1)
- gmx-saxs-legacy(1)
- gmx-covar(1)
- gmx-tcaf(1)
- gmx-filter(1)
- gmx-rms(1)
- gmx-bundle(1)
- gmx-vanhove(1)
- gmx-enemat(1)
- gmx-rama(1)
- gmx-spatial(1)
- gmx-nmens(1)
- gmx-mdmat(1)
- gmx-rotmat(1)
- gmx(1)
- gmx-eneconv(1)
- gmx-h2order(1)
- gmx-current(1)
- gmx-genion(1)
- gmx-rmsdist(1)
- gmx-report-methods(1)
- gmx-distance(1)
- gmx-insert-molecules(1)
- demux(1)
- gmx-dielectric(1)
- gmx-sans-legacy(1)
- gmx-sigeps(1)
- gmx-genrestr(1)
- gmx-analyze(1)
- gmx-convert-tpr(1)
- gmx-potential(1)
- gmx-wheel(1)
- gmx-mk_angndx(1)
- gmx-x2top(1)
- gmx-genconf(1)
- gmx-mindist(1)
- gmx-dipoles(1)
- gmx-polystat(1)
- gmx-hbond-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-make_ndx(1)
- gmx-nonbonded-benchmark(1)
- gmx-sham(1)
- gmx-nmr(1)
- xplor2gmx(1)
- gmx-densmap(1)
- gmx-bar(1)
- gmx-trajectory(1)
- gmx-sasa(1)
- gmx-dos(1)
- gmx-principal(1)
- gmx-pme_error(1)
- gmx-hbond(1)
- gmx-dump(1)
- gmx-traj(1)
- gmx-freevolume(1)
- gmx-trjconv(1)
- gmx_mpi(1)
- gmx-density(1)
- gmx-pdb2gmx(1)
- gmx-spol(1)
- gmx-cluster(1)
- gmx-select(1)
- gmx-rmsf(1)
- gmx-angle(1)
- gmx-saltbr(1)
- gmx-scattering(1)
- gmx-energy(1)
- gmx-dyecoupl(1)
- gmx-disre(1)
- gmx-pairdist(1)
- gmx-extract-cluster(1)
- gmx-tune_pme(1)
- gmx-check(1)
- gmx-nmtraj(1)
- gmx-helix(1)
- gmx-trjorder(1)
- gmx-grompp(1)
- gmx-gangle(1)
- gmx-dssp(1)
- gmx-convert-trj(1)
- gmx-sorient(1)
- gmx-chi(1)
- gmx-anaeig(1)
- gmx-lie(1)
- gmx-helixorient(1)
- gmx-mdrun(1)
- gmx-editconf(1)
- gmx-rdf(1)
- gmx_mpi_d(1)
- gmx-rotacf(1)
- gmx-nmeig(1)
- gmx-gyrate(1)
Package: gromacs-data
apt-get install gromacs-data
apt-get install gromacs-data
Manuals in package:
Documentations in package:
Manual
| 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
| May 12, 2025 | 2025.2 |