GROMACS

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GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research.^[1]^[2]

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 notably:

computation of the virial in a single, rather than in a double sum over particles,
generic representation of all possible periodic box types as triclinic,
optimized handling of the neighbor list by storage of translation vectors to the nearest neighbor in a periodic system,
a specialized routine for the calculation of the inverse square root,
the use of cubic spline interpolation from tabulated values for the evaluation of force/energy,
a fast grid-based neighbor searching,
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 force fields and the open source (GPL) nature of the project make GROMACS very flexible. A notable use of GROMACS is in the distributed computing project Folding@Home, where it is used extensively in the simulation of protein folding. (This version has been granted a non-GPL license.[1])

[edit] References

^ Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005). "GROMACS: fast, flexible, and free". J Comput Chem 26 (16): 1701–18. doi:10.1002/jcc.20291. PMID 16211538.
^ Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008). "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation". J Chem Theory Comput 4 (2): 435. doi:10.1021/ct700301q.