Dataset for "Assessing molecular simulation for the analysis of lipid monolayer reflectometry"

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".

Subjects:
Atomic and molecular physics
Biomolecules and biochemistry
Catalysis and surfaces
Materials sciences

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". University of Bath Research Data Archive. https://doi.org/10.15125/BATH-00586.

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Data

sim_vs_trad_data.zip
application/zip (6GB)
Creative Commons: Attribution-Share Alike 4.0

GitHub repository with code for full data analysis

Creators

Robert Grant
University of Bath

Andrew Smith
Diamond Light Source Ltd

Jonathan Rawle
Diamond Light Source Ltd

David Barlow
King's College London

M. Jayne Lawrence
University of Manchester

Stephen Parker
University of Bath

Karen Edler
University of Bath

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.

Documentation Files

README.md
text/plain (895B)
Creative Commons: Attribution-Share Alike 4.0

Funders

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 articles

McCluskey, A. R., Grant, J., Smith, A., Rawle, J., Barlow, D., Lawrence, J., Parker, S. C and Edler, K., 2019. Assessing molecular simulation for the analysis of lipid monolayer reflectometry. Journal of Physics Communications. 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. 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

Departments:

Faculty of Science
Chemistry