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GROMACS

GROMACS

GROMACS is a molecular dynamics simulator, with building and analysis tools.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

It provides extremely high performance compared to other competitors. A lot of algorithmic optimizations have been introduced in the code. The software is normally 3-10 times faster than any other program.

There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.

 GROMACS 5.0.5

Price
Free to download

Size
25.1MB
License

GNU GPL v2

Developer
David van der Spoel, Berk Hess, Erik Lindahl, and many contributors

Website
www.gromacs.org

System Requirements
10MB space (using shared libraries)

Support:
Wiki, Tutorials, HOWTOs, Mailing Lists, Facebook

Selected Reviews:
Journal of Computational Chemistry

Features include:

  • 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
  • There is no scripting language - all programs use a simple interface with command line options for input and output files
  • Extensive manuals provided free of charge in electronic or paper format.
  • 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. All files from GROMACS 2.0 can further be used in the new version 3
  • Write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user
  • 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
  • Can be run in parallel, using standard MPI communication
  • 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
  • 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

Return to Scientific Home Page | Return to Biology Tools Home Page

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Last Updated Saturday, May 23 2015 @ 12:45 PM EDT


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