GROMACS



GROMACS (GROningen MAchine for Chemical Simulations) is a Max Planck Institute for Polymer Research.

The GROMACS project was originally started to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture. The molecular dynamics specific routines were rewritten in the C programming language from the Fortran77-based program GROMOS, which had been developed in the same group. However, many specific elements were added, most notable among these being

  1. computation of the virial in a single, rather than a double, sum over particles,
  2. generic representation of all possible periodic box types as triclinic,
  3. optimized handling of the neighbour list by storage of translation vectors to the nearest neighbour in the periodic system,
  4. a specialized routine for the calculation of the inverse square root,
  5. the use of cubic spline interpolation from tabulated values for the evaluation of force/energy,
  6. a fast grid-based neighbour searching,
  7. the use of multimedia (3DNow! and SSE) instructions on Pentium (III and higher), Athlon, and Duron processors.

The highly optimized code makes GROMACS the fastest program for molecular simulations to date. In addition, support for different protein folding.

References

The content of this page is based on a recent article (Van der Spoel et al. Journal of Computational Chemistry 26: 1701 (2005))

See also


 
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