CHARMM36 POPC Lipid Bilayer Molecular Dynamics Simulation, 300 Nanoseconds

CHARMM36 POPC pure bilayer simulation provides a 300-nanosecond trajectory of a lipid membrane system at 300 Kelvin and 1 bar pressure. The data, created by Chris Papadopoulos of the Centre National de la Recherche Scientifique, contains the full simulation from 0 to 300 ns, sampled every 100 picoseconds and centered on phosphorus atoms. This bilayer was specifically used to calculate order parameters and area per lipid for the NMRlipids project.

Use Cases

• Validate lipid force field parameters based on the simulated bilayer structure.
• Calculate lipid order parameters for comparison with NMR experiments.
• Analyze area per lipid dynamics using the 50-300 ns time window.
• Study the behavior of a fully hydrated, charge-neutral membrane system.
• Benchmark molecular dynamics simulation protocols for membrane systems.

Strengths

• Simulation trajectory covers a full 300-nanosecond time range.
• System is fully defined with 256 POPC lipids and 34 water molecules per lipid.
• Trajectory is centered on phosphorus atoms, which likely simplifies structural analysis.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

Chris Papadopoulos, Centre National de la Recherche Scientifique

Collection Method

Molecular dynamics simulation using the CHARMM36 force field, with starting structure from CHARMM-GUI.

Time Range

0 to 300 nanoseconds