Optimized Simulation Conditions
The analysis of the various MD conformers in terms of secondary structures indicates that:
- Explicit lipids stabilize the helical segments.
- The packing of lipids around the transmembrane segments is better when a dielectric constant of 60 is used for SGB solvation.
The CRMS results indicate that NEIMO for helices and Cartesian for loop regions ( with lipids as rigid bodies and SGB dielectric constant = 60) gives the best description of the solution structure.