Dataset for "Assessing molecular simulation for the analysis of lipid monolayer reflectometry"
Reduced neutron reflectometry dataset associated with a contrast series of DSPC (distearoyl phosphatidylcholine) at the air-water interface. Molecular dynamics simulations at four different areas per molecule are included for three different force-fields. This dataset was used in the publication "Assessing molecular simulation for the analysis of lipid monolayer reflectometry".
Cite this dataset as:
McCluskey, A.,
Grant, R.,
Smith, A.,
Rawle, J.,
Barlow, D.,
Lawrence, M.,
Parker, S.,
Edler, K.,
2019.
Dataset for "Assessing molecular simulation for the analysis of lipid monolayer reflectometry".
Bath: University of Bath Research Data Archive.
Available from: https://doi.org/10.15125/BATH-00586.
Export
Data
sim_vs_trad_data.zip
application/zip (6GB)
Creative Commons: Attribution-Share Alike 4.0
Creators
Andrew McCluskey
University of Bath
Robert Grant
University of Bath
Andrew Smith
Diamond Light Source
Jonathan Rawle
Diamond Light Source
David Barlow
King's College London
M. Jayne Lawrence
University of Manchester
Stephen Parker
University of Bath
Karen Edler
University of Bath
Contributors
University of Bath
Rights Holder
Documentation
Data collection method:
Within this dataset are neutron reflectometry profiles that were collected at the ISIS Neutron and Muon Source, specifically the SURF instrument. Also within this dataset are the trajectories and input files for the molecular dynamics simulations of the lipid monolayers that were run using the GROMACS software.
Data processing and preparation activities:
The neutron reflectometry data are presented as received following the experiment and the on-site data reduction process.
Technical details and requirements:
For technical details for the neutron reflectometry experiment, please see Hollinshead et al., 2009 (DOI: 10.1021/la8028319). The .dat files are text files in space-separated value format. The molecular dynamics simulations were all run on the SCARF cluster at the RAL site, over 16 to 32 nodes. The production runs, that consist of 50 ns (simulation time) data, sampled every 0.1 ns. The GROMACS software (http://www.gromacs.org/) is required read the .cpt, .edr, .pdb, .tpr and .trr files. The .log and .gro files may be opened in a text editor. Please refer to the GROMACS reference manual for details of these file formats.
Methodology link:
Hollinshead, C. M., Harvey, R. D., Barlow, D. J., Webster, J. R. P., Hughes, A. V., Weston, A., and Lawrence, M. J., 2009. Effects of Surface Pressure on the Structure of Distearoylphosphatidylcholine Monolayers Formed at the Air/Water Interface. Langmuir, 25(7), 4070-4077. Available from: https://doi.org/10.1021/la8028319.
Lindahl, E., Abraham, M. J., Hess, B., and van der Spoel, D., 2019. GROMACS 2019.3 Manual. Version 2019.3. Zenodo. Available from: https://doi.org/10.5281/ZENODO.3243834.
Documentation Files
README.md
text/plain (895B)
Creative Commons: Attribution-Share Alike 4.0
Funders
University of Bath
https://doi.org/10.13039/501100000835
University of Bath and Diamond Light Source studentship
STU0149
Publication details
Publication date: 26 June 2019
by: University of Bath
Version: 1
DOI: https://doi.org/10.15125/BATH-00586
URL for this record: https://researchdata.bath.ac.uk/id/eprint/586
Related papers and books
McCluskey, A. R., Grant, J., Smith, A. J., Rawle, J. L., Barlow, D. J., Lawrence, M. J., Parker, S. C., and Edler, K. J., 2019. Assessing molecular simulation for the analysis of lipid monolayer reflectometry. Journal of Physics Communications, 3(7), 075001. Available from: https://doi.org/10.1088/2399-6528/ab12a9.
Related datasets and code
McCluskey, A. R., Grant, J., Smith, A. J., Rawle, J. L., Barlow, D. J., Lawrence, M. J., Parker, S. C., and Edler, K. J., 2019. sim_vs_trad. Version 1.0. Zenodo. Available from: https://doi.org/10.5281/ZENODO.3254719.
Contact information
Please contact the Research Data Service in the first instance for all matters concerning this item.
Contact person: Andrew McCluskey
Faculty of Science
Chemistry
