- After running MD Simulation do trajectory analysis
- Plot potential and kinetic energy over time. Should be pretty Constant
- remember to throw out the first part
- Kinetic is slightly positive
- Total Pe is very negative, total is negative
- Potential energy is sum of:
- Bond stretch (small)
- angle bending (small)
- dihedral alignment (small)
- improper (small)
- coulombic (easily largest contribution, very negative)
- vand der Waals (2nd largest, positive)
- Radial distribution functions (RDF)
- Density of atoms of a type within a spherical SHELL of radii R and thickness dr
- based on same reference atom, but do not have to search for same atom type (eg: Ca reference looking at water density)
- varying plot with r: initial spike, valley, then levels out in the middle
- All things should be equal as you get farther and it appears like the bulk value
- Example: N termini
- water density = 3.5 about 3 angstroms
- Example: C termini
- water density = 2 at about 3 angstroms
- Example: tyrosine beta carbon (hydrophobic)
- water density = 0.5 at 4 angstroms
- Example: tyrosine N terminus
- water density = 3.5 at 3 angstroms