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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. (Van der Spoel)
2008 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 3, 435-447 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 4, no 3, 435-447 p.
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-16716DOI: 10.1021/ct700301qISI: 000254277900007OAI: oai:DiVA.org:uu-16716DiVA: diva2:44487
Available from: 2008-06-03 Created: 2008-06-03 Last updated: 2017-12-08Bibliographically approved

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