EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-lie - Online in the Cloud

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

This is the command gmx-lie 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-lie - Estimate free energy from linear combinations

SYNOPSIS


gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-xvg <enum>] [-Elj <real>] [-Eqq <real>]
[-Clj <real>] [-Cqq <real>] [-ligand <string>]

DESCRIPTION


gmx lie computes a free energy estimate based on an energy analysis from nonbonded
energies. One needs an energy file with the following components: Coul-(A-B) LJ-SR (A-B)
etc.

To utilize g_lie correctly, two simulations are required: one with the molecule of
interest bound to its receptor and one with the molecule in water. Both need to utilize
energygrps such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr file.
Values from the molecule-in-water simulation are necessary for supplying suitable values
for -Elj and -Eqq.

OPTIONS


Options to specify input files:

-f [<.edr>] (ener.edr)
Energy file

Options to specify output files:

-o [<.xvg>] (lie.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

-Elj <real> (0)
Lennard-Jones interaction between ligand and solvent

-Eqq <real> (0)
Coulomb interaction between ligand and solvent

-Clj <real> (0.181)
Factor in the LIE equation for Lennard-Jones component of energy

-Cqq <real> (0.5)
Factor in the LIE equation for Coulomb component of energy

-ligand <string> (none)
Name of the ligand in the energy file

Use gmx-lie online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Cuckoo Sandbox
    Cuckoo Sandbox
    Cuckoo Sandbox uses components to
    monitor the behavior of malware in a
    Sandbox environment; isolated from the
    rest of the system. It offers automated
    analysis o...
    Download Cuckoo Sandbox
  • 2
    LMS-YouTube
    LMS-YouTube
    Play YouTube video on LMS (porting of
    Triode's to YouTbe API v3) This is
    an application that can also be fetched
    from
    https://sourceforge.net/projects/lms-y...
    Download LMS-YouTube
  • 3
    dotnet sdk
    dotnet sdk
    Core functionality needed to createNET
    Core projects, that is shared between
    Visual Studio and CLI. There are no fees
    or licensing costs, including for
    commerc...
    Download dotnet sdk
  • 4
    SportMusik
    SportMusik
    Mit dem Programm kann man schnell und
    einfach Pausen bei Sportveranstaltungen
    mit Musik überbrücken. Hierfür haben sie
    die Möglichkeit, folgende Wiedergabvaria...
    Download SportMusik
  • 5
    DavMail POP/IMAP/SMTP/Caldav to Exchange
    DavMail POP/IMAP/SMTP/Caldav to Exchange
    Ever wanted to get rid of Outlook ?
    DavMail is a
    POP/IMAP/SMTP/Caldav/Carddav/LDAP
    gateway allowing users to use any mail
    client with Exchange and Office 365, e...
    Download DavMail POP/IMAP/SMTP/Caldav to Exchange
  • 6
    DivFix++
    DivFix++
    DivFix++ is yours AVI video repair and
    preview software. It designed for repair
    and preview files which are on download
    from ed2k(emule), torrent, gnutella, ftp...
    Download DivFix++
  • 7
    JBoss Community
    JBoss Community
    Community driven projects featuring the
    latest innovations for cutting edge
    apps. Our flagship project JBoss AS is
    the leading Open Source,
    standards-compliant...
    Download JBoss Community
  • More »

Linux commands

Ad