CHARMM36 DPPE bilayer freezes at 342 K

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Singh, Avneesh;Ganguly, Anubhav;Miettinen, Markus S.

Description

This dataset contains MD simulation data of a system of a total of 34 DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) lipids in a bilayer (17 lipids per leaflet) using the CHARMM36 force field at 342 K. In addition to the lipid molecules, the system contains 1335 molecules of Charmm TIP3P water (39.3 waters / lipid). GROMACS version 2023.3 was used.Although the temperature is 7 degrees above the main transition temperature of DPPE (Tm = 335 K), the lipids are observed to enter the gel phase after roughly 30 ns of simulation. This is illustrated by the drop in area per lipid (see APL_vs_time.png), as well as the snapshots saved every 10 ns from the beginning (DPPE_342K_0ns.gro) to 100 ns (DPPE_342K_100ns.gro).The equilibrated trajectory file (DPPE_342K_100-200ns.xtc) covers the last 100 ns of the 200-ns trajectory, with coordinates saved every 15 ps.

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Metrics

Dataset Index

0.5

FAIR Score

85%

Citations

0

Mentions

0

Metrics Over Time

Publication Details

DOI

Publisher

Zenodo

License

Creative Commons Attribution 4.0 International

Assigned Domain

Subfield

Molecular Biology

Field

Biochemistry, Genetics and Molecular Biology

Domain

Life Sciences

Confidence Score

33%

Source

Scholar Data Model

Keywords

GROMACSLipidMolecular Dynamics SimulationLipid BilayerPhase TransitionGel PhaseModel Artefact

Normalization Factors

FT

53.85

CTw

1.00

MTw

1.00