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
    OfficeFloor
    OfficeFloor
    OfficeFloor provides inversion of
    coupling control, with its: - dependency
    injection - continuation injection -
    thread injection For more information
    visit the...
    Download OfficeFloor
  • 2
    DivKit
    DivKit
    DivKit is an open source Server-Driven
    UI (SDUI) framework. It allows you to
    roll out server-sourced updates to
    different app versions. Also, it can be
    used fo...
    Download DivKit
  • 3
    subconverter
    subconverter
    Utility to convert between various
    subscription format. Shadowrocket users
    should use ss, ssr or v2ray as target.
    You can add &remark= to
    Telegram-liked HT...
    Download subconverter
  • 4
    SWASH
    SWASH
    SWASH is a general-purpose numerical
    tool for simulating unsteady,
    non-hydrostatic, free-surface,
    rotational flow and transport phenomena
    in coastal waters as ...
    Download SWASH
  • 5
    VBA-M (Archived - Now on Github)
    VBA-M (Archived - Now on Github)
    Project has moved to
    https://github.com/visualboyadvance-m/visualboyadvance-m
    Features:Cheat creationsave statesmulti
    system, supports gba, gbc, gb, sgb,
    sgb2Tu...
    Download VBA-M (Archived - Now on Github)
  • 6
    Stacer
    Stacer
    Linux System Optimizer and Monitoring
    Github Repository:
    https://github.com/oguzhaninan/Stacer.
    Audience: End Users/Desktop. User
    interface: Qt. Programming La...
    Download Stacer
  • More »

Linux commands

Ad