Manual
User Manual:
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Page Count: 128 [warning: Documents this large are best viewed by clicking the View PDF Link!]
- Introduction
- Installation
- Running free-energy simulations
- Collective variables
- Absolute position
- Distance
- Minimum distance
- Angles
- Torsion
- Coordination number
- Hydrogen bonds
- Interfacial water
- Radius of gyration
- Dipole
- Dihedral correlation
- Alpha-beta similarity
- Alpharmsd
- Antibetarmsd
- Parabetarmsd
- Electrostatic potential
- Puckering coordinates
- Path collective variables
- Contact Map
- Energy
- Helix loops
- PCA projection
- SPRINT topological variables
- Radial distribution function
- Angular distribution function
- Polynomial combination of CVs
- Function of CVs
- A note on periodic boundary conditions
- Postprocessing