MacRog POPC Lipid Bilayer Molecular Dynamics Simulation, 500 Nanoseconds

A 500-nanosecond molecular dynamics simulation of a pure POPC lipid bilayer at 300 Kelvin and 1 bar pressure. The trajectory contains data from 0 to 500 ns, sampled every 100 picoseconds, and was created by modifying a CHARMM-GUI structure to match MacRog nomenclature. This simulation was used to calculate order parameters and area per lipid for the NMRLipids project.

Use Cases

• Validating lipid force field parameters based on the corrected `popc.itp` file.
• Calculating lipid order parameters based on the simulation trajectory.
• Analyzing area per lipid dynamics based on the 200-500 ns time window.
• Benchmarking simulation stability based on the 500 ns, fully hydrated system with 128 lipids.

Strengths

• Simulation covers a 500-nanosecond time window, suitable for equilibrium property analysis.
• System is fully hydrated with 40 water molecules per lipid for 128 POPC lipids.
• Provides a corrected `popc.itp` force field file with documented modifications.

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

Centre National de la Recherche Scientifique (CNRS)

Collection Method

Molecular dynamics simulation using a modified CHARMM-GUI structure.

Time Range

Simulation from 0 to 500 nanoseconds.