MD Simulations of PC/PS Lipid Bilayers with Calcium Chloride
by Jesper J. Madsen / University of Chicago
Available on 1 platform
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Description
NMRLipids IV project data comprises molecular dynamics simulations of a mixed lipid bilayer system. The dataset contains trajectories for a system of 250 POPC lipids, 50 POPS lipids, and 0.15M CaCl2, totaling 73,529 atoms, simulated using Gromacs and the CHARMM36 force field at 1 atm and 298K. It was contributed by Jesper J. Madsen of the University of Chicago.
Use Cases
Validate molecular dynamics force field parameters based on NMR data.
Study the structural effects of calcium ions on mixed phospholipid bilayers.
Analyze interactions between phosphatidylserine (POPS) lipids and divalent cations.
Benchmark simulation protocols for membrane systems containing charged lipids.
Strengths
Simulation details are explicitly stated, including 250 POPC lipids, 50 POPS lipids, and 0.15M CaCl2.
The system size is specified as containing 73,529 atoms.
Force field (CHARMM36), software (Gromacs), and thermodynamic conditions (1 atm, 298K) are documented.
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
NMRLipids IV project (nmrlipids.blogspot.fi), University of Chicago
Collection Method
Molecular dynamics simulation using Gromacs and the CHARMM36 force field.
Data format and specific file types are unknown; users may need to inspect the raw data after download.