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 | ||
B-factors | ||
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 |