EnglishFrenchSpanish

OnWorks favicon

gmx-check - Online in the Cloud

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

This is the command gmx-check 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-check - Check and compare files

SYNOPSIS


gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]]
[-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]]
[-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>]
[-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
[-abstol <real>] [-[no]ab] [-lastener <string>]

DESCRIPTION


gmx check reads a trajectory (.tng, .trr or .xtc), an energy file (.edr) or an index file
(.ndx) and prints out useful information about them.

Option -c checks for presence of coordinates, velocities and box in the file, for close
contacts (smaller than -vdwfac and not bonded, i.e. not between -bonlo and -bonhi, all
relative to the sum of both Van der Waals radii) and atoms outside the box (these may
occur often and are no problem). If velocities are present, an estimated temperature will
be calculated from them.

If an index file, is given its contents will be summarized.

If both a trajectory and a .tpr file are given (with -s1) the program will check whether
the bond lengths defined in the tpr file are indeed correct in the trajectory. If not you
may have non-matching files due to e.g. deshuffling or due to problems with virtual sites.
With these flags, gmx check provides a quick check for such problems.

The program can compare two run input (.tpr) files when both -s1 and -s2 are supplied.
Similarly a pair of trajectory files can be compared (using the -f2 option), or a pair of
energy files (using the -e2 option).

For free energy simulations the A and B state topology from one run input file can be
compared with options -s1 and -ab.

In case the -m flag is given a LaTeX file will be written consisting of a rough outline
for a methods section for a paper.

OPTIONS


Options to specify input files:

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

-f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng

-s1 [<.tpr>] (top1.tpr) (Optional)
Portable xdr run input file

-s2 [<.tpr>] (top2.tpr) (Optional)
Portable xdr run input file

-c [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent

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

-e2 [<.edr>] (ener2.edr) (Optional)
Energy file

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

Options to specify output files:

-m [<.tex>] (doc.tex) (Optional)
LaTeX file

Other options:

-vdwfac <real> (0.8)
Fraction of sum of VdW radii used as warning cutoff

-bonlo <real> (0.4)
Min. fract. of sum of VdW radii for bonded atoms

-bonhi <real> (0.7)
Max. fract. of sum of VdW radii for bonded atoms

-[no]rmsd (no)
Print RMSD for x, v and f

-tol <real> (0.001)
Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)

-abstol <real> (0.001)
Absolute tolerance, useful when sums are close to zero.

-[no]ab (no)
Compare the A and B topology from one file

-lastener <string>
Last energy term to compare (if not given all are tested). It makes sense to go up
until the Pressure.

Use gmx-check 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