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Gromacs

Company Name

Gromacs

Main Industry

Computer Equipment & Peripherals, Manufacturing

Website

www.gromacs.org

Gromacs Profile and History

GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or For tran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for i386 processors, separate versions using all x86-64 registers are used on Opteron x86-64 and Xeon EM64t machines. This results in exceptional performance on inexpensive PC workstations, and for Pentium IV/Opteron processors there are also SSE2 double precision assembly loops. There are new manually tuned assembly loops for ia64 (both single and double precision), and last but certainly not least we have written Altivec assembly loops both for Linux and Mac OS X. Gromacs is normally 3-10 timesfaster than any other program; check the article in Journal of Molecular Modeling (reference can be found under resources) for a comparison benchmark. GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading. There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs. As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished. Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user. GROMACS comes with a large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place! A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats. GROMACS can be run in parallel, using standard MPI communication. GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail. The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules. There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases. GROMACS is Free Software, available under the GNUGeneral Public License. A podcast of an interview with David van der Spoel about the past, present and future of GROMACS can be found here.

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Gromacs

Gromacs-core

manual.gromacs.org

Gromacs.org

tutorials.gromacs.org

Employees

28

Founded

1924

Top Gromacs Integrations and Technologies

Here's a list of some of the top trending technologies and APIs used by Gromacs.

Frameworks and Libraries

(2 Technologies)

Operating Systems

(2 Technologies)

Web Analytics

(1 Technologies)

Content Delivery Networks

(1 Technologies)

Web Hosting

(1 Technologies)

Gromacs Product Offerings

TechnologyWebsite UsingMarket Share
GPS Insight

GPS Insight

5

0.11%

GROMACS

GROMACS

38

<0.01%

Largest Customers of Gromacs Products

More than 5 companies reportedly use Gromacs products in their tech and software stacks

Gromacs Email Formats

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Your Questions, Our Answers

Get Free Access to Gromacs Contacts Info

How many employees does Gromacs have?

Gromacs has 28 employees

What are Gromacs’s primary industries?

Gromacs’s main industries are: Computer Equipment & Peripherals, Manufacturing

What are Gromacs’s key products?

Gromacs’s key products are: GPS Insight, GROMACS

What are some additional names or alternative spellings that users use while searching for Gromacs?

Gromacs appears in search results as Gromacs, Gromacs-core, manual.gromacs.orgGromacs.org, tutorials.gromacs.org...See More