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  Sharing data from molecular simulations.

Abraham, M. J., Apostolov, R. P., Barnoud, J., Bauer, P., Blau, C., Bonvin, A. M. J. J., et al. (2019). Sharing data from molecular simulations. Journal of Chemical Information and Modeling, 59(10), 4093-4099. doi:10.1021/acs.jcim.9b00665.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-B913-6 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-49E8-4
Genre: Journal Article

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 Creators:
Abraham, M. J., Author
Apostolov, R. P., Author
Barnoud, J., Author
Bauer, P., Author
Blau, C., Author
Bonvin, A. M. J. J., Author
Chavent, M., Author
Chodera, J. D., Author
Čondić-Jurkić, K., Author
Delemotte, L., Author
Grubmüller, H.1, Author              
Howard, R. J., Author
Jordan, E. J., Author
Lindal, E., Author
Ollila, O. H. S., Author
Selent, J., Author
Smith, D. G. A., Author
Stansfeld, P. J., Author
Tiemann, J. K. S., Author
Trellet, M., Author
Woods, C. J., AuthorZhmurov, A., Author more..
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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 Abstract: Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

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Language(s): eng - English
 Dates: 2019-09-172019
 Publication Status: Published in print
 Pages: -
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 Rev. Method: Peer
 Identifiers: DOI: 10.1021/acs.jcim.9b00665
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Title: Journal of Chemical Information and Modeling
Source Genre: Journal
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Pages: - Volume / Issue: 59 (10) Sequence Number: - Start / End Page: 4093 - 4099 Identifier: -