Change search
ReferencesLink to record
Permanent link

Direct link
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.
National Category
Other Physics Topics
URN: urn:nbn:se:kth:diva-48523DOI: 10.1002/wcms.50ISI: 000296005100005ScopusID: 2-s2.0-84855642902OAI: diva2:458723
Swedish eā€Science Research Center

QC 20111123

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

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Hess, Berk
By organisation
Theoretical & Computational Biophysics
Other Physics Topics

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 34 hits
ReferencesLink to record
Permanent link

Direct link