Comparing Simulations of Lipid Bilayers to Scattering Data: The GROMOS 43A1-S3 Force Field

• Published in: The journal of physical chemistry. B Vol. 117; no. 17; pp. 5065 - 5072
• Main Authors: Braun, Anthony R, Sachs, Jonathan N, Nagle, John F
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 02-05-2013
• Subjects: Acceptability; Biological and medical sciences; Compressibility; Computer simulation; Fundamental and applied biological sciences. Psychology; Lipid Bilayers - chemistry; Lipids; Molecular biophysics; Molecular Dynamics Simulation; Neutron Diffraction; Neutron scattering; Phosphatidylcholines - chemistry; Scattering; Simulation; X-Ray Diffraction; X-rays; Phospholipid; X ray scattering; Neutron scattering; Electron density; Modeling
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp401718k

Simulations of DOPC at T = 303 K were performed using the united atom force field 43A1-S3 at six fixed projected areas, A P = 62, 64, 66, 68, 70, and 72 Å2, as well as a tensionless simulation that produced an average A NPT = 65.8 Å2. After a small undulation correction for the system size consisting of 288 lipids, results were compared to experimental data. The best, and excellent, fit to neutron scattering data occurs at an interpolated A N = 66.6 Å2 and the best, but not as good, fit to the more extensive X-ray scattering data occurs at A X = 68.7 Å2. The distance ΔD B–H between the Gibbs dividing surface for water and the peak in the electron density profile agrees with scattering experiments. The calculated area compressibility K A = 277 ± 10 mN/m is in excellent agreement with the micromechanical experiment. The volume per lipid V L is smaller than volume experiments which suggests a workaround that raises all the areas by about 1.5%. Although A X ≠ A N ≠ A NPT, this force field obtains acceptable agreement with experiment for A L = 67.5 Å2 (68.5 Å2 in the workaround), which we suggest is a better DOPC result from 43A1-S3 simulations than its value from the tensionless NPT simulation. However, nonsimulation modeling obtains better simultaneous fits to both kinds of scattering data, which suggests that the force fields can still be improved.