Data · dataset · 2014
POPC @ 310K, model by Maciejewski and Rog
Listed in Zenodo
Input parameter file and part of the resulting trajectory for a POPC bilayer simulation.
Description
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].
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'. Note that this upload contains data every 100 ps between 30–110 ns of the simulation, whereas data every 10 ps in the interval 20–100 ns are employed in the results reported in the blog. This should have a diminishing effect on the results. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Files: md.tpr – run input file for Gromacs versions 4.6.3 and above md_100ps.xtc – The last 80 ns of a 110 ns long simulation.
Read the rest (2 more)
Data saved every 100 ps. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– [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. 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
- md.tpr zenodo.org/api/records/13497/files/md.tpr/content ↗
download · from Zenodo
- md_100ps.xtc zenodo.org/api/records/13497/files/md_100ps.xtc/content ↗
download · from Zenodo
Where it is published
- Zenodo record zenodo.org/records/13497 ↗
landing page · from Zenodo
- DOI doi.org/10.5281/zenodo.13497 ↗
DOI / persistent id · from Zenodo
Catalogue records · 1
- Zenodo API zenodo.org/api/records/13497 ↗
metadata API · from Zenodo
Topics
- Inferred from text
- Simulation 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Zenodo | 13497 | 15 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 |