In SuPepMem you can find different trajectory analyses such as:

• Number of contacts
• Peptide Analyses
• Lipid Analyses
• Density maps
• Lipid-Peptide Analyses

Number of contacts

Number of contacts between each residue of the peptide backbone and the different lipid types, averaged over the last microsecond and using a cut-off of 0.6 nm

Peptide Analyses

Peptide lateral displacement

Peptide lateral displacement along the trajectory, for different time windows

Peptide rotational displacement

Angle rotated by the peptide along the trajectory, for different time windows

Peptide Displacement Fingerprint (PepDF)

Lateral displacement vs Rotational Displacement along the trajectory, for different time windows

Tilt angle

Peptide tilt angle evolution, defined as the angle between the peptide helical axis and the bilayer normal

Hydrophobic dipolar moment

Electrostatic dipolar moment

Roll

Lipid Analyses

Area per lipid

Average area per lipid, per leaflet, along the trajectory

Density maps

2D-density maps along xy and zy axis, normalized and calculated for each lipid type, along the last microsecond. In this case, the trajectory was centered on the peptide

Lipid-Peptide Analyses

Z-Position

Z-coordinate, averaged for the different parts of the system: peptide, membrane, first and last backbone (BB) residue and upper or lower lipid headgroups (HG)

Minimum distance

Minimum distance (nm) between the peptide backbone and the water or lipids (headgroups and tailgroups)

Number of contacts

Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm

Lateral density

Lateral density for the components of the system, i.e. headgroups, tailgroups and the peptide