Package ffx.potential.nonbonded.implicit

Class NeckIntegral

java.lang.Object
ffx.potential.nonbonded.implicit.NeckIntegral
public class NeckIntegral extends Object
This class is used to compute interstitial space integrals of the form 1/r^6.

Inputs: radius of atom i (rho i) and radius of atom j (rho j) Outputs: Aij and Bij (interpolated/extrapolated from pre-determined tables)

Aij and Bij are constants used in the approximation of the 1/r^6 integral over pairwise neck regions described in Aguilar et. al. 2010. The neck integral approximation is as follows:

neck_integral(rij, rho i, rho j) = Aij * (rij - Bij)^4 * (rho i + rho j + 2 * rho w - rij)^4

Where rij is the separation distance between atoms i and j with radii rho i and rho j, respectively, and rho w is the radius of water (1.4 A).

Aij and Bij are determined for a set of discrete radii based on benchmark PB calculations of the maximum separation distance and neck integral value. Bij is set as 2*(maximum rij) - (rho i + rho j + 2 * rho w) and Aij is set such that the value of the neck integral approximation at the maximum separation distance matches the maximum neck integral value calculated using PB.

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. Perfect PB Born radii for rhoi = 1.7 Ang and rhoj = 1.7 Ang at a separation of 2.8 Ang probe = 0.0: 1.711784 Ang (avg of two) probe = 1.4: 1.750704 Ang (avg of two) Baseline Born radius values for rhoi = 1.7 Ang and rhoj = 1.7 Ang at a separation of 2.8 Ang using gk-radius vdw no neck correction, with descreen offset=0.3 Ang: 1.713269 Ang no neck correction, no descreen offset : 1.719362 Ang sneck=1.0, with descreen offset = 0.3 Ang: 1.738862 Ang sneck=1.0, no descreen offset : 1.755209 Ang

Since:
1.0
Author:
Rae A. Corrigan

  • Constructor Details

    • NeckIntegral

      public NeckIntegral()

  • Method Details

    • getNeckConstants

      public static double[] getNeckConstants(double rhoDescreened, double rhoDescreening)