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Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel.
To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes. Ca' Foscari University of Venice. Cagliari State University. Identity provider for the users of Free University of Bolzano.
Politecnico di Bari. Scuola Superiore Sant'Anna. University of Bologna.
University of Camerino. University of Genoa.
University of Messina. University of Naples Federico II. University of Padova. University of Palermo. University of Parma. University of Pavia.
University of Perugia. University of Pisa. University of Roma TRE. University of Rome Tor Vergata. University of Siena.
University of Verona.
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