EnglishFrenchSpanish

OnWorks favicon

gmx-clustsize - Online in the Cloud

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

This is the command gmx-clustsize 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-clustsize - Calculate size distributions of atomic clusters

SYNOPSIS


gmx clustsize [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
[-o [<.xpm>]] [-ow [<.xpm>]] [-nc [<.xvg>]]
[-mc [<.xvg>]] [-ac [<.xvg>]] [-hc [<.xvg>]]
[-temp [<.xvg>]] [-mcn [<.ndx>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
[-cut <real>] [-[no]mol] [-[no]pbc] [-nskip <int>]
[-nlevels <int>] [-ndf <int>] [-rgblo <vector>]
[-rgbhi <vector>]

DESCRIPTION


gmx clustsize computes the size distributions of molecular/atomic clusters in the gas
phase. The output is given in the form of an .xpm file. The total number of clusters is
written to an .xvg file.

When the -mol option is given clusters will be made out of molecules rather than atoms,
which allows clustering of large molecules. In this case an index file would still
contain atom numbers or your calculation will die with a SEGV.

When velocities are present in your trajectory, the temperature of the largest cluster
will be printed in a separate .xvg file assuming that the particles are free to move. If
you are using constraints, please correct the temperature. For instance water simulated
with SHAKE or SETTLE will yield a temperature that is 1.5 times too low. You can
compensate for this with the -ndf option. Remember to take the removal of center of mass
motion into account.

The -mc option will produce an index file containing the atom numbers of the largest
cluster.

OPTIONS


Options to specify input files:

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

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

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

Options to specify output files:

-o [<.xpm>] (csize.xpm)
X PixMap compatible matrix file

-ow [<.xpm>] (csizew.xpm)
X PixMap compatible matrix file

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

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

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

-hc [<.xvg>] (histo-clust.xvg)
xvgr/xmgr file

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

-mcn [<.ndx>] (maxclust.ndx) (Optional)
Index 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)

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-cut <real> (0.35)
Largest distance (nm) to be considered in a cluster

-[no]mol (no)
Cluster molecules rather than atoms (needs .tpr file)

-[no]pbc (yes)
Use periodic boundary conditions

-nskip <int> (0)
Number of frames to skip between writing

-nlevels <int> (20)
Number of levels of grey in .xpm output

-ndf <int> (-1)
Number of degrees of freedom of the entire system for temperature calculation. If
not set, the number of atoms times three is used.

-rgblo <vector> (1 1 0)
RGB values for the color of the lowest occupied cluster size

-rgbhi <vector> (0 0 1)
RGB values for the color of the highest occupied cluster size

Use gmx-clustsize online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    discussio...
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX
    GenX
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    pspp4windows
    pspp4windows
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands

Ad