Man page - gmx-densorder(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-DENSORDER(1) | GROMACS | GMX-DENSORDER(1) |
NAME
gmx-densorder - Calculate surface fluctuations
SYNOPSIS
gmx densorder [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-o [<.dat>]] [-or [<.out> [...]]] [-og [<.xpm> [...]]]
[-Spect [<.out> [...]]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-[no]1d] [-bw <real>]
[-bwn <real>] [-order <int>] [-axis <string>]
[-method <enum>] [-d1 <real>] [-d2 <real>]
[-tblock <int>] [-nlevel <int>]
DESCRIPTION
gmx densorder reduces a two-phase density distribution along an axis, computed over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a functional profile for interfacial densities. A time-averaged spatial representation of the interfaces can be output with the option -tavg.
OPTIONS
Options to specify input files:
- -s [<.tpr>] (topol.tpr)
- Portable xdr run input file
- -f [<.xtc/.trr/...>] (traj.xtc)
- Trajectory: xtc trr cpt gro g96 pdb tng
- -n [<.ndx>] (index.ndx)
- Index file
Options to specify output files:
- -o [<.dat>] (Density4D.dat) (Optional)
- Generic data file
- -or [<.out> [...]] (hello.out) (Optional)
- Generic output file
- -og [<.xpm> [...]] (interface.xpm) (Optional)
- X PixMap compatible matrix file
- -Spect [<.out> [...]] (intfspect.out) (Optional)
- Generic output file
Other options:
- -b <time> (0)
- Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
- Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
- Only use frame when t MOD dt = first time (default unit ps)
- -[no]w (no)
- View output .xvg, .xpm, .eps and .pdb files
- -[no]1d (no)
- Pseudo-1d interface geometry
- -bw <real> (0.2)
- Binwidth of density distribution tangential to interface
- -bwn <real> (0.05)
- Binwidth of density distribution normal to interface
- -order <int> (0)
- Order of Gaussian filter, order 0 equates to NO filtering
- -axis <string> (Z)
- Axis Direction - X, Y or Z
- -method <enum> (bisect)
- Interface location method: bisect, functional
- -d1 <real> (0)
- Bulk density phase 1 (at small z)
- -d2 <real> (1000)
- Bulk density phase 2 (at large z)
- -tblock <int> (100)
- Number of frames in one time-block average
- -nlevel <int> (100)
- Number of Height levels in 2D - XPixMaps
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 |