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GROMACS-the road ahead
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.ORCID iD: 0000-0002-7498-7763
2011 (English)In: WIRES COMPUT MOL SCI, 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
Wiley , 2011. Vol. 1, no 5, 710-715 p.
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Other Physics Topics
Identifiers
URN: urn:nbn:se:kth:diva-48523DOI: 10.1002/wcms.50ISI: 000296005100005Scopus ID: 2-s2.0-84855642902OAI: oai:DiVA.org:kth-48523DiVA: diva2:458723
Funder
Swedish eā€Science Research Center
Note

QC 20111123

Available from: 2011-11-23 Created: 2011-11-21 Last updated: 2016-04-20Bibliographically approved

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Hess, Berk

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