EnglishFrenchSpanish

OnWorks favicon

gmx-sorient - Online in the Cloud

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

This is the command gmx-sorient 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

PROGRAM:

NAME


gmx-sorient - Analyze solvent orientation around solutes

SYNOPSIS


gmx sorient [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-no [<.xvg>]] [-ro [<.xvg>]]
[-co [<.xvg>]] [-rc [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-[no]com] [-[no]v23]
[-rmin <real>] [-rmax <real>] [-cbin <real>]
[-rbin <real>] [-[no]pbc]

DESCRIPTION


gmx sorient analyzes solvent orientation around solutes. It calculates two angles between
the vector from one or more reference positions to the first atom of each solvent
molecule:

· theta_1: the angle with the vector from the first atom of the solvent molecule to the
midpoint between atoms 2 and 3.

· theta_2: the angle with the normal of the solvent plane, defined by the same three
atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and
3.

The reference can be a set of atoms or the center of mass of a set of atoms. The group of
solvent atoms should consist of 3 atoms per solvent molecule. Only solvent molecules
between -rmin and -rmax are considered for -o and -no each frame.

-o: distribution of cos(theta_1) for rmin<=r<=rmax.

-no: distribution of cos(theta_2) for rmin<=r<=rmax.

-ro: <cos(theta_1)> and <3cos(^2theta_2)-1> as a function of the distance.

-co: the sum over all solvent molecules within distance r of cos(theta_1) and
3cos(^2(theta_2)-1) as a function of r.

-rc: the distribution of the solvent molecules as a function of r

OPTIONS


Options to specify input files:

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

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

-no [<.xvg>] (snor.xvg)
xvgr/xmgr file

-ro [<.xvg>] (sord.xvg)
xvgr/xmgr file

-co [<.xvg>] (scum.xvg)
xvgr/xmgr file

-rc [<.xvg>] (scount.xvg)
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

-[no]com (no)
Use the center of mass as the reference position

-[no]v23 (no)
Use the vector between atoms 2 and 3

-rmin <real> (0)
Minimum distance (nm)

-rmax <real> (0.5)
Maximum distance (nm)

-cbin <real> (0.02)
Binwidth for the cosine

-rbin <real> (0.02)
Binwidth for r (nm)

-[no]pbc (no)
Check PBC for the center of mass calculation. Only necessary when your reference
group consists of several molecules.

Use gmx-sorient online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Firebird
    Firebird
    Firebird RDBMS offers ANSI SQL features
    & runs on Linux, Windows &
    several Unix platforms. Features
    excellent concurrency & performance
    & power...
    Download Firebird
  • 2
    KompoZer
    KompoZer
    KompoZer is a wysiwyg HTML editor using
    the Mozilla Composer codebase. As
    Nvu's development has been stopped
    in 2005, KompoZer fixes many bugs and
    adds a f...
    Download KompoZer
  • 3
    Free Manga Downloader
    Free Manga Downloader
    The Free Manga Downloader (FMD) is an
    open source application written in
    Object-Pascal for managing and
    downloading manga from various websites.
    This is a mirr...
    Download Free Manga Downloader
  • 4
    UNetbootin
    UNetbootin
    UNetbootin allows you to create bootable
    Live USB drives for Ubuntu, Fedora, and
    other Linux distributions without
    burning a CD. It runs on Windows, Linux,
    and ...
    Download UNetbootin
  • 5
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM is an easy to use
    ERP and CRM open source software package
    (run with a web php server or as
    standalone software) for businesses,
    foundations...
    Download Dolibarr ERP - CRM
  • 6
    SQuirreL SQL Client
    SQuirreL SQL Client
    SQuirreL SQL Client is a graphical SQL
    client written in Java that will allow
    you to view the structure of a JDBC
    compliant database, browse the data in
    tables...
    Download SQuirreL SQL Client
  • More »

Linux commands

Ad