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Theory

Disclaimer: this section is for ANA's developers reference. It does not contain relevant information for the users.

Spring constant

Adaptations used to calculate cavity flexibility from Amber mass-weighted eigenvalues.

where,

  • ν: frequency in units of 1/s
  • λ^{amber}: amber frequencies in units of 1/cm
  • c: speed of light
  • constants added to adjust cm to angstroms and Kg to g

where,

  • ω: angular frequency in units of 1/s

where,

  • λ^{NMA}: spring constant k for a NMA vector
  • m: mass (doesn't matter as long as units are correct)

In units of Kcal/mol

Rigidity constant

In units of KJ/mol

Rigidity constant

Amber PCA eigenvalues to quasi-harmonic analysis frequencies

From equipartition theorem:

In Amber from angstroms^2 to cm^-1 in Kcal/mol, at 300K:

  • λ_{amber i}: amber frequencies in units of 1/cm
  • λ_{PCA i}: amber PCA eigenvalues in units of Å^{2}
  • constant added to adjust Å to cm^{-1}