Data · dataset · 2014
POPC @ 310K, varying water-to-lipid ratio. Model by Maciejewski and Rog
Listed in Zenodo
Input parameter files and parts of the resulting trajectories for a POPC bilayer simulation with varying water-to-lipid ratios.
Description
The used ratios are 50, 25, 20, 15, 10, and 5. The force field is an extension to the OPLS-based force field by the same authors [1].
The same POPC force field has also been employed in [2]. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Files: XX.tpr – XX waters per lipid; run input file for Gromacs versions 4.5.5 and above. XXWperL_YYns.xtc – The last YY ns of a 100 or 90 ns long simulation (50 ns discarded from the beginning). XX waters per lipid. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– This data is used in the project "Matching lipid force fields with NMR data", see: nmrlipids.blogspot.fi and referred to in the blog as 'MacRog' [1] Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., and Rog, T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration.
Read the rest (2 more)
The Journal of Physical Chemistry B 118 , 4571–4581 (2014). DOI: 10.1021/jp5016627 [2] Kulig, W., Jurkiewicz, P., Olzynska, A., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Hof, M., Vattulainen, I. and Jungwirth, P. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. Biochimica et Biophysica Acta (BBA) - Biomembranes 1848 , 422–432 (2015).
DOI: 10.1016/j.bbamem.2014.10.032
Links
Get the data
- 15.tpr zenodo.org/api/records/13498/files/15.tpr/content ↗
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- 5.tpr zenodo.org/api/records/13498/files/5.tpr/content ↗
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- 10WperL_50ns.xtc zenodo.org/api/records/13498/files/10WperL_50ns.xtc/content ↗
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- 10.tpr zenodo.org/api/records/13498/files/10.tpr/content ↗
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- 15WperL_50ns.xtc zenodo.org/api/records/13498/files/15WperL_50ns.xtc/content ↗
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- 50WperL_40ns.xtc zenodo.org/api/records/13498/files/50WperL_40ns.xtc/content ↗
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- 25.tpr zenodo.org/api/records/13498/files/25.tpr/content ↗
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- 25WperL_50ns.xtc zenodo.org/api/records/13498/files/25WperL_50ns.xtc/content ↗
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- 5WperL_50ns.xtc zenodo.org/api/records/13498/files/5WperL_50ns.xtc/content ↗
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- 20.tpr zenodo.org/api/records/13498/files/20.tpr/content ↗
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- 50.tpr zenodo.org/api/records/13498/files/50.tpr/content ↗
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- 20WperL_50ns.xtc zenodo.org/api/records/13498/files/20WperL_50ns.xtc/content ↗
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Where it is published
- Zenodo record zenodo.org/records/13498 ↗
landing page · from Zenodo
- DOI doi.org/10.5281/zenodo.13498 ↗
DOI / persistent id · from Zenodo
Catalogue records · 1
- Zenodo API zenodo.org/api/records/13498 ↗
metadata API · from Zenodo
Topics
- Inferred from text
- Simulation 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Zenodo | 13498 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · Zenodo | connector:zenodo@1.0.0 | /metadata/access_right |
| byte_size | source · Zenodo | connector:zenodo@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · Zenodo | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · Zenodo | connector:zenodo@1.0.0 | |
| description | source · Zenodo | connector:zenodo@1.0.0 | /metadata/description |
| license_text | source · Zenodo | connector:zenodo@1.0.0 | |
| publication_date | source · Zenodo | connector:zenodo@1.0.0 | |
| title | source · Zenodo | connector:zenodo@1.0.0 | /metadata/title |
| updated_date | source · Zenodo | connector:zenodo@1.0.0 |