Archive · dataset · 2015
Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014
Listed in Zenodo
MD simulation files 72 hydrated DPPC + 2189 water TIP3P NPgT P=1atm, gamma=0, T=323K (liquid crystalline phase) 20 ns equilibration (not here) 50 ns trajectory (dcd file) Model : Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB.
Description
CHARMM36 United Atom Chain Model for Lipids and Surfactants. J Phys Chem B . 2014;118(2):547-556. doi:10.1021/jp410344g. ----
- bilayer-72DPPC-c36-AU.psf : NAMD2.10 structure file Obtained with psfgen utility, using 1) topology from Lee et al. 2014 2) positions from J. Klauda. terpconnect.umd.edu/~jbklauda/research/download.html ----
- dppc_c36_AU.equil.2.dcd : trajectory file of 2635 frames every 20 ps. ---
- measure_SCD_heads.tcl : file used to measure order parameters for the head hydrogens using vmd-1.9 --- *namd_input.tar files usefull to launch the simulations using NAMD(2.10).
Links
Get the data
- namd_input.tar zenodo.org/api/records/17004/files/namd_input.tar/content ↗
download · from Zenodo
- dppc_c36_AU.equil.2.dcd zenodo.org/api/records/17004/files/dppc_c36_AU.equil.2.dcd/content ↗
download · from Zenodo
- measure_SCD_heads.tcl zenodo.org/api/records/17004/files/measure_SCD_heads.tcl/content ↗
download · from Zenodo
- bilayer-72DPPC-c36-AU.psf zenodo.org/api/records/17004/files/bilayer-72DPPC-c36-AU.psf/content ↗
download · from Zenodo
Where it is published
- Zenodo record zenodo.org/records/17004 ↗
landing page · from Zenodo
- DOI doi.org/10.5281/zenodo.17004 ↗
DOI / persistent id · from Zenodo
Catalogue records · 1
- Zenodo API zenodo.org/api/records/17004 ↗
metadata API · from Zenodo
Topics
- Inferred from text
- Simulation 75%
Related
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Zenodo | 17004 | 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 |