Package ffx.potential.nonbonded.implicit

Class BornTanhRescaling

java.lang.Object
ffx.potential.nonbonded.implicit.BornTanhRescaling
public class BornTanhRescaling extends Object
Rescale the Born radius integral to account for interstitial spaces.

Ri^-1 = [rhoi^-3 - (4*pi/3(rhoi^-3 - 50^-3)) * tanh(beta0*Psi*rhoi^3 - beta1*(Psi*rhoi^3)^2 + beta2*(Psi*rhoi^3)^3)]^(1/3)

Citations: Aguilar, B.; Shadrach, R.; Onufriev, A. V. Reducing the secondary structure bias in the generalized Born model via R6 effective radii. J. Chem. Theory Comput. 2010, 6, 3613−3630.

Onufriev, A.; Bashford, D.; Case, D. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004, 55, 383−394.

Since:
1.0
Author:
Rae A. Corrigan

  • Field Details

    • MAX_BORN_RADIUS

      public static final double MAX_BORN_RADIUS
      Maximum Born radius.
      See Also:

  • Constructor Details

    • BornTanhRescaling

      public BornTanhRescaling()

  • Method Details

    • tanhRescaling

      public static double tanhRescaling(double Ii, double rhoi)
      Rescale the Born radius integral to account for interstitial spaces.
      Parameters:
      Ii - The total integral of 1/r^6 over vdW spheres and pairwise neck integrals.
      rhoi - The base radius of for the atom being descreened.
      Returns:
      The rescaled integral, which is greater than or equal to the input integral.

    • tanhRescalingChainRule

      public static double tanhRescalingChainRule(double Ii, double rhoi)
      The chain rule derivative for rescaling the Born radius integral to account for interstitial spaces.
      Parameters:
      Ii - The total integral of 1/r^6 over vdW spheres and pairwise neck integrals.
      rhoi - The base radius of for the atom being descreened.
      Returns:
      The chain rule derivative.

    • getBeta0

      public static double getBeta0()

    • getBeta1

      public static double getBeta1()

    • getBeta2

      public static double getBeta2()

    • setBeta0

      public static void setBeta0(double beta0)

    • setBeta1

      public static void setBeta1(double beta1)

    • setBeta2

      public static void setBeta2(double beta2)