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Contents:

  • Introduction
  • Simulation control options
    • General information
    • Run control
    • Model parameter
    • Temperature coupling
    • Pressure coupling
    • Periodic boundary condition:
    • File input/output
    • Simulation platform
    • Restart simulation
  • Parameters
    • Note on hps (lambda) in urry scale:
  • System
  • Models
    • Coarse grained, alpha-carbon (CA), model
    • The Bonded potential:
    • Angle Potential
    • Torsion Potential
    • The Pairwise potential:
    • The Debye-Huckle potential has following form:
  • Dynamics
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