uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
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
Identifiers
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

Open Access in DiVA

No full text

Other links

Publisher's full text

Authority records BETA

van der Spoel, David

Search in DiVA

By author/editor
van der Spoel, David
By organisation
Computational and Systems Biology
Natural Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 354 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf