Current & Prospective Modules

We will keep adding modules but not limited to following lists

Modules Description Status
System size Analyzing changes of system size during simulations. done
Density profile Analyzing the density based on the number of atoms with given axis and bin size. All, Lipid head, Lipid tail, Water, Water dipole, vector and Custom selection are available. done
Lipid deuterium order parameters Calculating deuterium order parameters of selected atoms. CHARMM format is currently available. done
Root-mean-squared deviation Analyzing root-mean-square deviation. done
Root-mean-squared fluctuation Analyzing root-mean-square fluctuations. done
Lipid hydrophobic thickness Estimating the thickness of membrane. Thickness based on Phosphate, Carbon, and custom selection are available. done
Lipid surface area Calculating area of individual lipids and overall average surface area of lipid. Area is calculated by utilizing Voronoi diagram. done
Sterol tilt angle Analyzing the tilt angle of sterols with respect to the bilayer normal. Ring tilt and tail tilt are available done
Helix (ß-hairpin) tilt, rotation,crossing angles, and distance Calculating helix (ß-hairpin) tilt and rotation angles as well as helix-helix (ß-hairpin-ß-hairpin) crossing angle and distance in progress
Secondary structure
Dihedral angles
Distance between two atoms
H-bond / salt-bridge profile
Residue-residue contacts
Solid-state NMR properties (chemical shift, dipolar coupling constant)
Channel pore size
Membrane potential
Water/ion movement
Lipid lateral diffusion constant
Lipid chain relaxation time
Lipid rotation/wobble motions
Lateral ion density inside channel
Residue-water/lipid contact information
Solvent accessible surface area
Lipid adaptation (through selection of "local" and "bulk" lipids)
Substrate binding
Pore hydration