Alchemical free energy calculations and umbrella sampling with local molecular field theory

2018 ◽  
Vol 17 (03) ◽  
pp. 1840003 ◽  
Author(s):  
Richard C. Remsing ◽  
John D. Weeks

Understanding the thermodynamic driving forces underlying any chemical process requires a description of the underlying free energy surface. However, computation of free energies is difficult, often requiring advanced sampling techniques. Moreover, these computations can be further complicated by the evaluation of any long-ranged interactions in the system of interest, such as Coulomb interactions in charged and polar media. Local molecular field theory is a promising approach to avoid many of the conceptual and computational difficulties associated with long-ranged interactions. We present frameworks for performing alchemical free energy calculations and non-Boltzmann sampling with local molecular field theory. We demonstrate that local molecular field theory can be used to perform these free energy calculations with accuracy comparable to traditional methodologies while eliminating the need for explicit treatment of long-ranged interactions in simulations.

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.


2019 ◽  
Vol 123 (27) ◽  
pp. 5671-5677 ◽  
Author(s):  
Rodrigo Aguayo-Ortiz ◽  
Augusto González-Navejas ◽  
Giovanni Palomino-Vizcaino ◽  
Oscar Rodriguez-Meza ◽  
Miguel Costas ◽  
...  

2020 ◽  
Vol 60 (11) ◽  
pp. 5407-5423 ◽  
Author(s):  
Gerhard König ◽  
Nina Glaser ◽  
Benjamin Schroeder ◽  
Alžbeta Kubincová ◽  
Philippe H. Hünenberger ◽  
...  

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