OnWorks favicon

gmx-make_ndx - Online in the Cloud

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

This is the command gmx-make_ndx 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



gmx-make_ndx - Make index files


gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]]
[-natoms <int>] [-[no]twin]


Index groups are necessary for almost every GROMACS program. All these programs can
generate default index groups. You ONLY have to use gmx make_ndx when you need SPECIAL
index groups. There is a default index group for the whole system, 9 default index groups
for proteins, and a default index group is generated for every other residue name.

When no index file is supplied, also gmx make_ndx will generate the default groups. With
the index editor you can select on atom, residue and chain names and numbers. When a run
input file is supplied you can also select on atom type. You can use NOT, AND and OR, you
can split groups into chains, residues or atoms. You can delete and rename groups.

The atom numbering in the editor and the index file starts at 1.

The -twin switch duplicates all index groups with an offset of -natoms, which is useful
for Computational Electrophysiology double-layer membrane setups.


Options to specify input files:

-f [<.gro/.g96/...>] (conf.gro) (Optional)
Structure file: gro g96 pdb brk ent esp tpr

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

Options to specify output files:

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

Other options:

-natoms <int> (0)
set number of atoms (default: read from coordinate or index file)

-[no]twin (no)
Duplicate all index groups with an offset of -natoms

Use gmx-make_ndx online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    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
    Download Eclipse Tomcat Plugin
  • 2
    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
  • 3
    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
  • 4
    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
  • 5
    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
  • 6
    eSpeak: speech synthesis
    eSpeak: speech synthesis
    Text to Speech engine for English and
    many other languages. Compact size with
    clear but artificial pronunciation.
    Available as a command-line program with
    many ...
    Download eSpeak: speech synthesis
  • More »

Linux commands