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GROMACS: the road ahead
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2011 (English)In: Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, Vol. 1, no 5, 710-715 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in 'real time', and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made.

Place, publisher, year, edition, pages
2011. Vol. 1, no 5, 710-715 p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-161952DOI: 10.1002/wcms.50ISI: 000296005100005OAI: oai:DiVA.org:uu-161952DiVA: diva2:457968
Available from: 2011-11-21 Created: 2011-11-21 Last updated: 2011-11-21Bibliographically approved

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van der Spoel, David
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