MD Simulations of POPC/POPS Lipid Bilayers with Calcium Chloride

250 POPC and 50 POPS lipids were simulated with 1M CaCl2 using Gromacs and the CHARMM36 force field. The simulation was run at 1 atmosphere and 298 Kelvin for 200 nanoseconds, containing 73,964 atoms. This dataset was produced by Jesper J. Madsen at the University of Chicago as part of the NMRLipids IV project.

Use Cases

• Analyzing lipid bilayer structure and dynamics based on the 200-nanosecond molecular dynamics trajectory.
• Studying calcium ion binding to phosphatidylserine (POPS) lipids in mixed membranes.
• Validating force field parameters for lipid mixtures against experimental NMR data.
• Investigating membrane properties like area per lipid and order parameters from the simulation data.

Strengths

• Simulation details are explicitly specified, including 250 POPC and 50 POPS lipids, 1M CaCl2 concentration, and 73,964 atoms.
• The force field (CHARMM36), software (Gromacs), and thermodynamic conditions (1 atm, 298K) are clearly stated.
• The simulation length of 200 nanoseconds provides a substantial trajectory for analysis.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• The description notes 'no pre-equilibration', which may affect the initial state of the simulation.
• Row count and file formats are unknown, which may limit suitability assessment.

Provenance

Source

University of Chicago, NMRLipids IV project (nmrlipids.blogspot.fi)

Collection Method

Molecular dynamics simulation using Gromacs and the CHARMM36 force field.