EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-angle - Online in the Cloud

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

This is the command gmx-angle 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-angle - Calculate distributions and correlations for angles and dihedrals

SYNOPSIS


gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]
[-ov [<.xvg>]] [-of [<.xvg>]] [-ot [<.xvg>]] [-oh [<.xvg>]]
[-oc [<.xvg>]] [-or [<.trr>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-xvg <enum>] [-type <enum>]
[-[no]all] [-binwidth <real>] [-[no]periodic]
[-[no]chandler] [-[no]avercorr] [-acflen <int>]
[-[no]normalize] [-P <enum>] [-fitfn <enum>]
[-beginfit <real>] [-endfit <real>]

DESCRIPTION


gmx angle computes the angle distribution for a number of angles or dihedrals.

With option -ov, you can plot the average angle of a group of angles as a function of
time. With the -all option, the first graph is the average and the rest are the individual
angles.

With the -of option, gmx angle also calculates the fraction of trans dihedrals (only for
dihedrals) as function of time, but this is probably only fun for a select few.

With option -oc, a dihedral correlation function is calculated.

It should be noted that the index file must contain atom triplets for angles or atom
quadruplets for dihedrals. If this is not the case, the program will crash.

With option -or, a trajectory file is dumped containing cos and sin of selected dihedral
angles, which subsequently can be used as input for a principal components analysis using
gmx covar.

Option -ot plots when transitions occur between dihedral rotamers of multiplicity 3 and
-oh records a histogram of the times between such transitions, assuming the input
trajectory frames are equally spaced in time.

OPTIONS


Options to specify input files:

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

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

Options to specify output files:

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

-ov [<.xvg>] (angaver.xvg) (Optional)
xvgr/xmgr file

-of [<.xvg>] (dihfrac.xvg) (Optional)
xvgr/xmgr file

-ot [<.xvg>] (dihtrans.xvg) (Optional)
xvgr/xmgr file

-oh [<.xvg>] (trhisto.xvg) (Optional)
xvgr/xmgr file

-oc [<.xvg>] (dihcorr.xvg) (Optional)
xvgr/xmgr file

-or [<.trr>] (traj.trr) (Optional)
Trajectory in portable xdr format

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

-type <enum> (angle)
Type of angle to analyse: angle, dihedral, improper, ryckaert-bellemans

-[no]all (no)
Plot all angles separately in the averages file, in the order of appearance in the
index file.

-binwidth <real> (1)
binwidth (degrees) for calculating the distribution

-[no]periodic (yes)
Print dihedral angles modulo 360 degrees

-[no]chandler (no)
Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine
correlation function. Trans is defined as phi < -60 or phi > 60.

-[no]avercorr (no)
Average the correlation functions for the individual angles/dihedrals

-acflen <int> (-1)
Length of the ACF, default is half the number of frames

-[no]normalize (yes)
Normalize ACF

-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

-beginfit <real> (0)
Time where to begin the exponential fit of the correlation function

-endfit <real> (-1)
Time where to end the exponential fit of the correlation function, -1 is until the
end

KNOWN ISSUES


· Counting transitions only works for dihedrals with multiplicity 3

Use gmx-angle online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    XyZerKunG ServerTool
    XyZerKunG ServerTool
    XyZerKunG ServerTool helps you to make
    your own Minecraft server and play with
    your friend for a few minutes.
    Features:Automatically create a
    Minecraft serverU...
    Download XyZerKunG ServerTool
  • 2
    CalcTools
    CalcTools
    Java source intended to serve as a
    nexus for teaching both mathematics and
    software solutions for computation on
    iterative equations. Public interfaces
    allow a...
    Download CalcTools
  • 3
    Rocket.Chat Desktop Client
    Rocket.Chat Desktop Client
    Rocket.Chat Desktop client is the
    official desktop app for Rocket.Chat,
    the simple but powerful open source web
    chat platform. It's tested on macOS,
    Windows...
    Download Rocket.Chat Desktop Client
  • 4
    OfficeFloor
    OfficeFloor
    OfficeFloor provides inversion of
    coupling control, with its: - dependency
    injection - continuation injection -
    thread injection For more information
    visit the...
    Download OfficeFloor
  • 5
    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
  • 6
    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
  • More »

Linux commands

Ad