MD Simulations of PC/PS Lipid Bilayers with Calcium Chloride

NMRLipids IV project molecular dynamics simulations of a mixed lipid bilayer system. The dataset contains trajectories for a system of 250 POPC and 50 POPS lipids with calcium chloride, simulated for 200 nanoseconds at 298 Kelvin and 1 atmosphere using Gromacs and the CHARMM36 force field. The data was contributed by Jesper J. Madsen of the University of Chicago.

Use Cases

• Analyzing lipid bilayer structure and dynamics based on the 200-nanosecond simulation trajectory.
• Studying calcium ion interactions with phosphatidylserine (POPS) lipids in mixed membranes.
• Validating molecular dynamics force fields for lipid systems based on the CHARMM36 parameters.
• Investigating the effects of lipid composition on membrane properties based on the 250:50 POPC:POPS ratio.

Strengths

• Simulation details are explicitly provided, including the 200-nanosecond duration, 298K temperature, and 1 atm pressure.
• System composition is precisely defined with 250 POPC and 50 POPS lipids, totaling 73,521 atoms.
• Uses established simulation software (Gromacs) and a widely-used force field (CHARMM36).

Limitations

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

Provenance

Source

NMRLipids IV project (nmrlipids.blogspot.fi)

Collection Method

Molecular dynamics simulation using Gromacs software and the CHARMM36 force field.