EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-disre - Online in the Cloud

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

This is the command gmx-disre 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-disre - Analyze distance restraints

SYNOPSIS


gmx disre [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-c [<.ndx>]] [-ds [<.xvg>]] [-da [<.xvg>]] [-dn [<.xvg>]]
[-dm [<.xvg>]] [-dr [<.xvg>]] [-l [<.log>]] [-q [<.pdb>]]
[-x [<.xpm>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
[-xvg <enum>] [-ntop <int>] [-maxdr <real>]
[-nlevels <int>] [-[no]third]

DESCRIPTION


gmx disre computes violations of distance restraints. The program always computes the
instantaneous violations rather than time-averaged, because this analysis is done from a
trajectory file afterwards it does not make sense to use time averaging. However, the time
averaged values per restraint are given in the log file.

An index file may be used to select specific restraints for printing.

When the optional -q flag is given a .pdb file coloured by the amount of average
violations.

When the -c option is given, an index file will be read containing the frames in your
trajectory corresponding to the clusters (defined in another manner) that you want to
analyze. For these clusters the program will compute average violations using the third
power averaging algorithm and print them in the log file.

OPTIONS


Options to specify input files:

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

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

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

-c [<.ndx>] (clust.ndx) (Optional)
Index file

Options to specify output files:

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

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

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

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

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

-l [<.log>] (disres.log)
Log file

-q [<.pdb>] (viol.pdb) (Optional)
Protein data bank file

-x [<.xpm>] (matrix.xpm) (Optional)
X PixMap compatible matrix 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

-ntop <int> (0)
Number of large violations that are stored in the log file every step

-maxdr <real> (0)
Maximum distance violation in matrix output. If less than or equal to 0 the maximum
will be determined by the data.

-nlevels <int> (20)
Number of levels in the matrix output

-[no]third (yes)
Use inverse third power averaging or linear for matrix output

Use gmx-disre online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

Linux commands

  • 1
    abidw
    abidw
    abidw - serialize the ABI of an ELF
    file abidw reads a shared library in ELF
    format and emits an XML representation
    of its ABI to standard output. The
    emitted ...
    Run abidw
  • 2
    abilint
    abilint
    abilint - validate an abigail ABI
    representation abilint parses the native
    XML representation of an ABI as emitted
    by abidw. Once it has parsed the XML
    represe...
    Run abilint
  • 3
    createhdf
    createhdf
    createhdf Create a blank IDE hard
    disk image inhdf format ...
    Run createhdf
  • 4
    CreateInterface
    CreateInterface
    CreateInterface Create a Java
    Interface definition from DBus
    introspection data. ...
    Run CreateInterface
  • 5
    gba3
    gba3
    gba3 - GAMBAS Archiver ...
    Run gba3
  • 6
    gbackground
    gbackground
    gbackground - interval-based gnome
    background changer SYNTAX: gbackground
    DESCRIPTION: This program allows to
    change periodically the gnome background
    in inter...
    Run gbackground
  • More »

Ad