scholarly journals Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*

2019 ◽  
Author(s):  
Robert E. Duke ◽  
G. Andres Cisneros
Keyword(s):  
Force Field ◽  
Electrostatic Model ◽  
Integral Evaluation ◽  
Gaussian Integral ◽  
And Performance

Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit.

Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*

2019 ◽  
Author(s):  
Robert E. Duke ◽  
G. Andres Cisneros
Keyword(s):  
Force Field ◽  
Electrostatic Model ◽  
Integral Evaluation ◽  
Gaussian Integral ◽  
And Performance

Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit.

Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*

2019 ◽  
Author(s):  
Robert E. Duke ◽  
G. Andres Cisneros
Keyword(s):  
Force Field ◽  
Electrostatic Model ◽  
Integral Evaluation ◽  
Gaussian Integral ◽  
And Performance

Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit.

scholarly journals Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*

2019 ◽  
Author(s):  
Robert E. Duke ◽  
G. Andres Cisneros
Keyword(s):  
Force Field ◽  
Electrostatic Model ◽  
Integral Evaluation ◽  
Gaussian Integral ◽  
And Performance

Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit.

scholarly journals Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

2020 ◽  
Author(s):  
Rae Corrigan ◽  
Guowei Qi ◽  
Andrew Thiel ◽  
Jack Lynn ◽  
Brandon Walker ◽  
...  
Keyword(s):  
Force Field ◽  
Protein Design ◽  
Numerical Solutions ◽  
Target Function ◽  
Model Parameters ◽  
Implicit Solvent ◽  
Electrostatic Model ◽  
Implicit Solvents ◽  
Poisson Boltzmann Equation ◽  
Amoeba Force Field

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>

scholarly journals An optimized charge penetration model for use with the AMOEBA force field

2017 ◽  
Vol 19 (1) ◽  
pp. 276-291 ◽  
Author(s):  
Joshua A. Rackers ◽  
Qiantao Wang ◽  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Force Field ◽  
Short Range ◽  
Electrostatic Model ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base ◽  
Range Error ◽  
Amoeba Force Field

Inclusion of charge penetration corrects the short-range error in the electrostatic model of the AMOEBA force field, and improves the accuracy of interactions ranging from nucleic acid base stacking to protein–ligand binding.

Sign in / Sign up

Export Citation Format

Share Document