OnWorks favicon

gmx-order - Online in the Cloud

Run gmx-order in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-order that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



gmx-order - Compute the order parameter per atom for carbon tails


gmx order [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-nr [<.ndx>]]
[-s [<.tpr>]] [-o [<.xvg>]] [-od [<.xvg>]] [-ob [<.pdb>]]
[-os [<.xvg>]] [-Sg [<.xvg>]] [-Sk [<.xvg>]]
[-Sgsl [<.xvg>]] [-Sksl [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-d <enum>] [-sl <int>]
[-[no]szonly] [-[no]unsat] [-[no]permolecule] [-[no]radial]


gmx order computes the order parameter per atom for carbon tails. For atom i the vector
i-1, i+1 is used together with an axis. The index file should contain only the groups to
be used for calculations, with each group of equivalent carbons along the relevant acyl
chain in its own group. There should not be any generic groups (like System, Protein) in
the index file to avoid confusing the program (this is not relevant to tetrahedral order
parameters however, which only work for water anyway).

gmx order can also give all diagonal elements of the order tensor and even calculate the
deuterium order parameter Scd (default). If the option -szonly is given, only one order
tensor component (specified by the -d option) is given and the order parameter per slice
is calculated as well. If -szonly is not selected, all diagonal elements and the deuterium
order parameter is given.

The tetrahedrality order parameters can be determined around an atom. Both angle an
distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys.,
93, (1998), 511-518. for more details.


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx)
Index file

-nr [<.ndx>] (index.ndx)
Index file

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

Options to specify output files:

-o [<.xvg>] (order.xvg)
xvgr/xmgr file

-od [<.xvg>] (deuter.xvg)
xvgr/xmgr file

-ob [<.pdb>] (eiwit.pdb)
Protein data bank file

-os [<.xvg>] (sliced.xvg)
xvgr/xmgr file

-Sg [<.xvg>] (sg-ang.xvg) (Optional)
xvgr/xmgr file

-Sk [<.xvg>] (sk-dist.xvg) (Optional)
xvgr/xmgr file

-Sgsl [<.xvg>] (sg-ang-slice.xvg) (Optional)
xvgr/xmgr file

-Sksl [<.xvg>] (sk-dist-slice.xvg) (Optional)
xvgr/xmgr file

Other options:

-b <time> (0)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-d <enum> (z)
Direction of the normal on the membrane: z, x, y

-sl <int> (1)
Calculate order parameter as function of box length, dividing the box into this
number of slices.

-[no]szonly (no)
Only give Sz element of order tensor. (axis can be specified with -d)

-[no]unsat (no)
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed
with normal order parameters.

-[no]permolecule (no)
Compute per-molecule Scd order parameters

-[no]radial (no)
Compute a radial membrane normal

-[no]calcdist (no)
Compute distance from a reference

Use gmx-order online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Alt-F provides a free and open source
    alternative firmware for the DLINK
    DNS-320/320L/321/323/325/327L and
    DNR-322L. Alt-F has Samba and NFS;
    supports ext2/3/4...
    Download Alt-F
  • 2
    Usm is a unified slackware package
    manager that handles automatic
    dependency resolution. It unifies
    various package repositories including
    slackware, slacky, p...
    Download usm
  • 3
    Chart.js is a Javascript library that
    allows designers and developers to draw
    all kinds of charts using the HTML5
    canvas element. Chart js offers a great
    array ...
    Download Chart.js
  • 4
    iReport-Designer for JasperReports
    iReport-Designer for JasperReports
    NOTE: iReport/Jaspersoft Studio Support
    Announcement: As of version 5.5.0,
    Jaspersoft Studio will be the official
    design client for JasperReports. iReport
    Download iReport-Designer for JasperReports
  • 5
    PostInstallerF will install all the
    software that Fedora Linux and others
    doesn't include by default, after
    running Fedora for the first time. Its
    easy for...
    Download PostInstallerF
  • 6
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • More »

Linux commands