Pure POPC Membrane Molecular Dynamics Simulations with CHARMM-Drude Force Field

400 ns of molecular dynamics simulation data of a pure POPC membrane, comprising 40000 frames saved every 10 ps. The dataset, created by Batuhan Kav of Forschungszentrum Jülich, uses the CHARMM-Drude force field in OpenMM 7.5.0 and includes 64 POPC lipids per leaflet and 6400 SWM4-NPD water molecules. A corrected trajectory file with proper timestamps is provided.

Use Cases

• Validate the CHARMM-Drude force field's performance for lipid bilayers based on the provided simulation trajectories.
• Analyze membrane properties like area per lipid and thickness based on the 400 ns production data.
• Benchmark simulation analysis workflows using the corrected timestamp information in the wrapped_full.xtc file.
• Study lipid-water interactions using the specified count of 6400 SWM4-NPD water molecules.

Strengths

• Includes a substantial 400 ns of production simulation data after discarding 100 ns for equilibration.
• Provides a corrected trajectory file (wrapped_full.xtc) with accurate timestamps, addressing a known issue.
• Specifies precise system composition: 64 POPC lipids per leaflet and 6400 SWM4-NPD water molecules.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.
• The original DCD trajectory file had incorrect timestamp information, though a corrected version is supplied.

Provenance

Source

Forschungszentrum Jülich

Collection Method

Molecular dynamics simulation using OpenMM 7.5.0 with the CHARMM-Drude force field.