GROMACS

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GROMACS

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Basic data

developer KTH Stockholm ,
Uppsala University
u. a.
Current  version 2018
(Jan. 11, 2018)
operating system Windows , macOS , Linux
programming language C.
category Simulation software
License GNU GPL
German speaking No
www.gromacs.org

GROMACS ( Gro ningen Ma chine for C hemical S imulations ) is a software package for simulation and analysis of molecular dynamics processes (MD), which originally developed at the University of Groningen has been developed. Today, the support and development takes place in various locations and facilities, including the University of Uppsala , Stockholm University and the Max Planck Institute for Polymer Research .

properties

The GROMACS project was originally started in the early 1990s to construct an optimized parallel computer system for molecular simulation. The whole system was initially based on a ring-shaped architecture of the participating computers with complex communication between the individual nodes. The specific routines were based on the GROMOS program , which was developed in the same working group in Groningen. But they were rewritten in C , whereas GROMOS was written in Fortran 77. In addition, a variety of specific elements have been added, e.g. B .:

  • a special routine to the complex square root to get around
  • optimized processing of the list of neighboring atoms
  • Calculation of the virial equation as a single instead of a double sum over the particles
  • fast grid based search for neighboring atoms
  • Use of multimedia ( 3DNow and SSE ) commands on Pentium (III and higher), Athlon and Duron processors.
  • Use of OpenCL and CUDA for GPU and MPI for computer networks with version 5 or 2016 and higher.

The continuously optimized code makes GROMACS one of the fastest programs in the field of molecular simulations currently available (as of July 2009). In addition, GROMACS becomes very flexible through the support of various force fields such as AMBER , OPLS or GROMOS. The distribution under GPL licensing is another point worth mentioning from GROMACS. This type of licensing means that the package is already included in many Linux distributions or can be easily installed later. For distributed computing, MPI support is available as an option during installation. The Folding @ home project at Stanford University uses GROMACS under a non-GPL license in the area of ab initio simulations of protein folding. The package includes almost 100 programs for performing and analyzing molecular dynamic calculations.

See also

Web links

Individual evidence

  1. ↑ The GROMACS developers. In: gromacs.org. Retrieved October 6, 2017 .
  2. ↑ GROMACS on Windows. In: gromacs.org. Retrieved October 6, 2017 .
  3. ↑ The gromacs Open Source Project on Open Hub: Languages Page . In: Open Hub . (accessed on July 18, 2018).
  4. ↑ Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ: GROMACS: fast, flexible, and free . In: J Comput Chem . tape 26 , no. 16 , 2005, pp. 1701-18 , doi : 10.1002 / jcc.20291 , PMID 16211538 .
  5. ↑ Hess B, Kutzner C, Van Der Spoel D, Lindahl E: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation . In: J Chem Theory Comput . tape 4 , no. 2 , 2008, p. 435 , doi : 10.1021 / ct700301q .